☰ Navigation Tabs
Crystal structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 100 mM MES pH 6.2
100 mM calcium chloride
5% ethylene glycol
20% PEG Smear Broad
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.012 α = 90 b = 154.846 β = 98.043 c = 85.451 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91578 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.86 84.61 94 0.073 0.1 0.998 8.9 3.5 96340 37.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.97 82 0.912 0.47 1.1 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ZUJ 1.865 84.6 96297 4830 93.91 0.178 0.1762 0.2074 0.1968 37.903
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] -0.245 0.231 0.293 -0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.249 r_dihedral_angle_4_deg 22.343 r_dihedral_angle_3_deg 15.291 r_lrange_it 11.187 r_dihedral_angle_1_deg 6.162 r_scangle_it 4.707 r_mcangle_it 3.407 r_scbond_it 3.189 r_mcbond_it 2.279 r_angle_refined_deg 1.669
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.249 r_dihedral_angle_4_deg 22.343 r_dihedral_angle_3_deg 15.291 r_lrange_it 11.187 r_dihedral_angle_1_deg 6.162 r_scangle_it 4.707 r_mcangle_it 3.407 r_scbond_it 3.189 r_mcbond_it 2.279 r_angle_refined_deg 1.669 r_symmetry_xyhbond_nbd_refined 0.326 r_nbtor_refined 0.314 r_symmetry_nbd_refined 0.264 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.239 r_metal_ion_refined 0.171 r_symmetry_metal_ion_refined 0.117 r_chiral_restr 0.114 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9472 Nucleic Acid Atoms Solvent Atoms 1053 Heterogen Atoms 179
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing