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Crystal structure of human serine racemase in complex with DSiP fragment Z126932614, 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 2.11 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.112 α = 90 b = 154.937 β = 97.957 c = 85.539 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 0.91587 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 1.599 84.716 97.6 0.059 0.082 0.997 8.9 3.3 158956 29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.599 1.63 93.4 0.658 0.889 0.383 1.1 2.7
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 1.6 84.7 158845 7962 97.468 0.173 0.1722 0.1982 0.1899 28.988
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] -0.11 0.112 0.195 -0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.046 r_dihedral_angle_4_deg 24.948 r_dihedral_angle_3_deg 14.963 r_lrange_it 10.177 r_dihedral_angle_1_deg 6.233 r_scangle_it 4.302 r_mcangle_it 3.109 r_scbond_it 2.879 r_mcbond_it 2.002 r_angle_refined_deg 1.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.046 r_dihedral_angle_4_deg 24.948 r_dihedral_angle_3_deg 14.963 r_lrange_it 10.177 r_dihedral_angle_1_deg 6.233 r_scangle_it 4.302 r_mcangle_it 3.109 r_scbond_it 2.879 r_mcbond_it 2.002 r_angle_refined_deg 1.882 r_nbtor_refined 0.317 r_symmetry_xyhbond_nbd_refined 0.313 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.203 r_xyhbond_nbd_refined 0.189 r_metal_ion_refined 0.168 r_chiral_restr 0.127 r_symmetry_metal_ion_refined 0.056 r_bond_refined_d 0.013 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9445 Nucleic Acid Atoms Solvent Atoms 920 Heterogen Atoms 218
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing