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Crystal Structure of Serine Racemase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FKP PDB ENTRY 1FKP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.261 α = 90 b = 102.96 β = 90 c = 120.923 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2008-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.0332 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 41.1 95.8 0.069 0.069 10.1 3.17 34466 32657 2 2 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 74.8 0.195 0.195 3.5 1.95 1837
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FKP 2.1 41.1 2 2 34466 32657 1795 95.77 0.24389 0.24136 0.24 0.28949 0.2876 RANDOM 29.478
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.297 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 14.354 r_dihedral_angle_1_deg 5.242 r_scangle_it 1.34 r_angle_refined_deg 0.993 r_scbond_it 0.771 r_mcangle_it 0.739 r_mcbond_it 0.402 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.297 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 14.354 r_dihedral_angle_1_deg 5.242 r_scangle_it 1.34 r_angle_refined_deg 0.993 r_scbond_it 0.771 r_mcangle_it 0.739 r_mcbond_it 0.402 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4844 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 32
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling