THEORETICAL AND PHYSICAL CHEMISTRY
CONTENTS CHAPTER CRYSTALLIZING A PROTEIN INTRODUCTION PRINCIPLES OF PROTEIN CRYSTALLIZATION CRYSTALLIZATION TECHNIQUES CRYSTALLIZATION OF LYSOZYME A PRELIMINARY NOTE ON CRYSTALS PREPARATION FOR AN X-RAY DIFFRACTION EXPERIMENT CRYOCOOLING NOTES SUMMARY CHAPTER X-RAY SOURCES AND DETECTORS X-RAY SOURCES MONOCHROMATORS INTRODUCTION TO CAMERAS AND DETECTORS DETECTORS THE ROTATION (OSCILLATION) INSTRUMENT CRYSTALS SYMMETRY POSSIBLE SYMMETRY FOR PROTEIN CRYSTALS COORDINATE TRIPLETS: GENERAL AND SPECIAL POSITIONS ASYMMETRIC UNIT POINT GROUPS CRYSTAL SYSTEMS RADIATION DAMAGE CHARACTERIZATION OF THE CRYSTALS THEORY OF X-RAY DIFFRACTION BY A CRYSTAL WAVES AND THEIR ADDITION A SYSTEM OF TWO ELECTRONS SCATTERING BY AN ATOM SCATTERING BY A UNIT CELL SCATTERING BY A CRYSTAL DIFFRACTION CONDITIONS RECIPROCAL LATTICE AND EWALD CONSTRUCTION THE TEMPERATURE FACTOR CALCULATION OF THE ELECTRON DENSITY (X Y Z) COMPARISON OF F(H K L) AND F( ¯H ¯K ¯L) SYMMETRY IN THE DIFFRACTION PATTERN INTEGRAL RE?ECTION CONDITIONS FOR CENTERED LATTICES INTENSITY DIFFRACTED BY A CRYSTAL SCATTERING BY A PLANE OF ATOMS CHOICE OF WAVELENGTH, SIZE OF UNIT CELL, AND CORRECTION OF THE DIFFRACTED INTENSITY AVERAGE RE?ECTION INTENSITY AND DISTRIBUTION OF STRUCTURE FACTOR DATA AVERAGE INTENSITY; WILSON PLOTS THE DISTRIBUTION OF STRUCTURE FACTORS F AND STRUCTURE FACTOR AMPLITUDES |F| CRYSTAL TWINNING SPECIAL FORMS OF THE STRUCTURE FACTOR THE UNITARY STRUCTURE FACTOR THE NORMALIZED STRUCTURE FACTOR THE SOLUTION OF THE PHASE PROBLEM BY THE ISOMORPHOUS REPLACEMENT METHOD THE PATTERSON FUNCTION THE ISOMORPHOUS REPLACEMENT METHOD EFFECT OF HEAVY ATOMS ON X-RAY INTENSITIES DETERMINATION OF THE HEAVY ATOM PARAMETERS FROM CENTROSYMMETRIC PROJECTIONS PARAMETERS OF HEAVY ATOMS DERIVED FROM ACENTRIC RE?ECTIONS THE DIFFERENCE FOURIER SUMMATION ANOMALOUS SCATTERING THE ANOMALOUS PATTERSON SUMMATION ONE COMMON ORIGIN FOR ALL DERIVATIVES RE?NEMENT OF THE HEAVY ATOM PARAMETERS USING PRELIMINARY PROTEIN PHASE ANGLES PROTEIN PHASE ANGLES THE REMAINING ERROR IN THE BEST FOURIER MAP THE SINGLE ISOMORPHOUS REPLACEMENT METHOD PHASE IMPROVEMENT THE OMIT MAP WITH AND WITHOUT SIM WEIGHTING SOLVENT FLATTENING NONCRYSTALLOGRAPHIC SYMMETRY AND MOLECULAR AVERAGING HISTOGRAM MATCHING WARP: WEIGHTED AVERAGING OF MULTIPLE-RE?NED DUMMY ATOMIC MODELS FURTHER CONSIDERATIONS CONCERNING DENSITY MODI?CATION ANOMALOUS SCATTERING IN THE DETERMINATION OF THE PROTEIN PHASE ANGLES AND THE ABSOLUTE CON?GURATION PROTEIN PHASE ANGLE DETERMINATION WITH ANOMALOUS SCATTERING IMPROVEMENT OF PROTEIN PHASE ANGLES WITH ANOMALOUS SCATTERING THE DETERMINATION OF THE ABSOLUTE CON?GURATION MULTIPLE- AND SINGLE-WAVELENGTH ANOMALOUS DIFFRACTION (MAD AND SAD) MOLECULAR REPLACEMENT THE ROTATION FUNCTION THE TRANSLATION FUNCTION DIRECT METHODS SHAKE-AND-BAKE SHELXD THE PRINCIPLE OF MAXIMUM ENTROPY LAUE DIFFRACTION THE ACCESSIBLE REGION OF RECIPROCAL SPACE THE MULTIPLE PROBLEM UNSCRAMBLING OF MULTIPLE INTENSITIES THE SPATIAL OVERLAP PROBLEM WAVELENGTH NORMALIZATION RE?NEMENT OF THE MODEL STRUCTURE THE MATHEMATICS OF RE?NEMENT THE PRINCIPLE OF THE FAST FOURIER TRANSFORM METHOD SPECI?C RE?NEMENT METHODS THE COMBINATION OF PHASE INFORMATION PHASE INFORMATION FROM ISOMORPHOUS REPLACEMENT PHASE INFORMATION FROM ANOMALOUS SCATTERING PHASE INFORMATION FROM PARTIAL STRUCTURE DATA, SOLVENT FLATTENING, AND MOLECULAR AVERAGING PHASE INFORMATION FROM SAD CHECKING FOR GROSS ERRORS AND ESTIMATING THE ACCURACY OF THE STRUCTURAL MODEL R-FACTORS THE RAMACHANDRAN PLOT STEREOCHEMISTRY CHECK THE 3D–1D PRO?LE METHOD QUANTITATIVE ESTIMATION OF THE COORDINATE ERROR IN THE FINAL MODEL PRACTICAL PROTEIN CRYSTALLIZATION GENE CLONING AND EXPRESSION PROTEIN PURI?CATION PROTEIN CRYSTALLIZATION