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Crystal structure of human serine racemase in complex with DSiP fragment Z2856434779, 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 = 48.15 α = 90 b = 154.86 β = 98.08 c = 85.48 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) Rpim 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 1.71 77.6 98.2 0.067 0.093 0.997 8.3 3.4 130785
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 1.71 1.74 97.2 0.948 0.305 1 2.9
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 1.71 77.4 130740 6527 98.094 0.176 0.1744 0.1744 0.2015 0.2015 32.375
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] -0.361 0.225 0.417 -0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.742 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 14.537 r_lrange_it 9.728 r_dihedral_angle_1_deg 6.459 r_scangle_it 3.003 r_mcangle_it 2.493 r_scbond_it 1.924 r_mcbond_it 1.483 r_angle_refined_deg 1.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.742 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 14.537 r_lrange_it 9.728 r_dihedral_angle_1_deg 6.459 r_scangle_it 3.003 r_mcangle_it 2.493 r_scbond_it 1.924 r_mcbond_it 1.483 r_angle_refined_deg 1.356 r_nbtor_refined 0.311 r_symmetry_xyhbond_nbd_refined 0.239 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.216 r_metal_ion_refined 0.165 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.099 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9507 Nucleic Acid Atoms Solvent Atoms 867 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing