☰ Navigation Tabs
X-ray crystal structure of human 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 2.15 42.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.57 α = 90 b = 84.29 β = 90 c = 69.98 γ = 90
Symmetry Space Group P 21 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 100 CCD ADSC QUANTUM 315 MIRROR 2008-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97960 Diamond I04
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 1.5 38.32 99 0.049 0.049 13.9 3.7 52035 2 1.5 15.9
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) 1.5 1.58 100 0.275 0.275 4.4 3.7 49358
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 1.5 36.11 1.5 2 49358 49358 2649 98.6 0.161 0.161 0.16 0.1846 0.177 0.1947 RANDOM 12.53
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] 0.05 -0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.297 r_dihedral_angle_4_deg 13.949 r_dihedral_angle_3_deg 11.217 r_dihedral_angle_1_deg 5.263 r_scangle_it 3.17 r_scbond_it 2.18 r_mcangle_it 1.525 r_angle_refined_deg 1.169 r_mcbond_it 0.965 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.297 r_dihedral_angle_4_deg 13.949 r_dihedral_angle_3_deg 11.217 r_dihedral_angle_1_deg 5.263 r_scangle_it 3.17 r_scbond_it 2.18 r_mcangle_it 1.525 r_angle_refined_deg 1.169 r_mcbond_it 0.965 r_nbtor_refined 0.302 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.137 r_xyhbond_nbd_refined 0.111 r_symmetry_hbond_refined 0.081 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2432 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 23
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling