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X-ray crystal structure of rat serine racemase in complex with malonate a potent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other HUMAN SERINE RACEMASE SOLVED BY SELENOMETHIONINE SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.593 α = 90 b = 110.593 β = 90 c = 47.917 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2008-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.54187
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 2.2 55.29 97.7 0.06 0.06 9.4 2.5 30389 30389 2 3 38.2
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) 2.2 2.33 83.4 0.311 0.311 2.1 1.55 30389
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 (All) 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 HUMAN SERINE RACEMASE SOLVED BY SELENOMETHIONINE SAD 2.2 47.89 2 1.5 30389 30285 1586 95.9 0.219 0.219 0.216 0.2206 0.267 0.2676 RANDOM 47.64
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] -0.04 -0.02 -0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.731 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_3_deg 17.685 r_dihedral_angle_1_deg 6.844 r_scangle_it 3.071 r_scbond_it 1.983 r_angle_refined_deg 1.604 r_mcangle_it 1.417 r_mcbond_it 0.806 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.731 r_dihedral_angle_4_deg 17.842 r_dihedral_angle_3_deg 17.685 r_dihedral_angle_1_deg 6.844 r_scangle_it 3.071 r_scbond_it 1.983 r_angle_refined_deg 1.604 r_mcangle_it 1.417 r_mcbond_it 0.806 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.097 r_symmetry_hbond_refined 0.064 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4779 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 46
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling