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Crystal structure of human serine racemase in complex with DSiP fragment Z26781964, 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 = 48.18 α = 90 b = 154.88 β = 98.04 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) 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 1.77 51.6 97.1 0.072 0.098 0.997 8.2 3.4 116780
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 1.77 1.82 96.3 1.048 0.302 1 3.3
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 1.77 47.752 116737 5859 97.001 0.171 0.1694 0.1695 0.2018 0.2019 35.476
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] -0.385 0.29 0.588 -0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.999 r_dihedral_angle_4_deg 21.461 r_dihedral_angle_3_deg 14.906 r_lrange_it 10.565 r_dihedral_angle_1_deg 6.755 r_scangle_it 4.863 r_scbond_it 3.446 r_mcangle_it 3.332 r_mcbond_it 2.343 r_angle_refined_deg 1.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.999 r_dihedral_angle_4_deg 21.461 r_dihedral_angle_3_deg 14.906 r_lrange_it 10.565 r_dihedral_angle_1_deg 6.755 r_scangle_it 4.863 r_scbond_it 3.446 r_mcangle_it 3.332 r_mcbond_it 2.343 r_angle_refined_deg 1.734 r_nbtor_refined 0.31 r_symmetry_nbd_refined 0.276 r_symmetry_xyhbond_nbd_refined 0.227 r_nbd_refined 0.221 r_metal_ion_refined 0.192 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.116 r_bond_refined_d 0.013 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9435 Nucleic Acid Atoms Solvent Atoms 975 Heterogen Atoms 250
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing