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PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH PHOSPHITE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRJ PDB ENTRY 2PRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 289 T-STATE PYRIDOXAL PHOSPHORYLASE B, FROM RABBIT MUSCLE, WAS CO-CRYSTALLIZED WITH 8-10 MM FLUOROPHOSPHATE IN A MEDIUM CONSISTING OF 15-25 MG/ML ENZYME, 2 MM IMP, 2 MM SPERMINE, 50 MM GLUCOSE, 10 MM BES, 0.1 MM EDTA, AND 0.02% SODIUM AZIDE, PH 6.7 (16 DEGREE C). JUST BEFORE DATA COLLECTION, THE CRYSTALS WERE TRANSFERRED TO A FRESH BUFFER SOLUTION, CONTAINING THE SAME CONSTITUENTS AS THEIR MOTHER LIQUOR WITH THE EXCEPTION OF THE PROTEIN., VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.47 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.5 α = 90 b = 128.5 β = 90 c = 116.3 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 FILM 1993-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX7.2 SRS PX7.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.46 16.88 84.89 0.074 3.039 30529 30529
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.57 65
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PRJ 2.46 16.88 30529 30529 84.89 0.168 0.168 0.218 RANDOM
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.5 x_angle_deg 1.4 x_improper_angle_d 0.72 x_bond_d 0.008 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.5 x_angle_deg 1.4 x_improper_angle_d 0.72 x_bond_d 0.008 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6749 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 50
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement MOSCO data reduction CCP4 data scaling X-PLOR phasing