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Crystal structure of human serine racemase in complex with DSiP fragment Z52314092, 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 2.09 41.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.11 α = 90 b = 154.76 β = 98.14 c = 85.4 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 2018-07-15 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 1.53 77.4 95.9 0.052 0.075 0.998 9 3.2 177718
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 1.53 1.57 87 0.804 0.453 2.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ZUJ 1.53 77.38 177667 8706 95.829 0.183 0.1823 0.1819 0.202 0.2016 28.092
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] -0.039 0.601 -0.461 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.717 r_dihedral_angle_4_deg 18.352 r_dihedral_angle_3_deg 13.136 r_lrange_it 8.238 r_dihedral_angle_1_deg 6.075 r_scangle_it 1.946 r_mcangle_it 1.699 r_scbond_it 1.22 r_angle_refined_deg 1.151 r_mcbond_it 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.717 r_dihedral_angle_4_deg 18.352 r_dihedral_angle_3_deg 13.136 r_lrange_it 8.238 r_dihedral_angle_1_deg 6.075 r_scangle_it 1.946 r_mcangle_it 1.699 r_scbond_it 1.22 r_angle_refined_deg 1.151 r_mcbond_it 0.99 r_nbtor_refined 0.307 r_symmetry_xyhbond_nbd_refined 0.255 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.214 r_metal_ion_refined 0.177 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.087 r_symmetry_metal_ion_refined 0.063 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9368 Nucleic Acid Atoms Solvent Atoms 941 Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing