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Human serine racemase holoenzyme from 20% DMSO soak (XChem crystallographic fragment screen).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SLH
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 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.062 α = 90 b = 154.998 β = 98.26 c = 85.652 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 2018-07-13 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) 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 1.8 84.764 97.8 0.068 0.081 0.043 0.997 9.46 3.41 111815
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 95.61 0.704 0.829 0.436 0.651 1.69 3.54
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 6SLH 1.8 84.764 111681 5508 97.639 0.181 0.1789 0.1789 0.2198 0.2198 34.405
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] 0.012 0.528 -0.247 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.181 r_dihedral_angle_4_deg 21.498 r_dihedral_angle_3_deg 14.485 r_lrange_it 9.435 r_dihedral_angle_1_deg 6.449 r_scangle_it 2.579 r_mcangle_it 2.325 r_scbond_it 1.635 r_mcbond_it 1.39 r_angle_refined_deg 1.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.181 r_dihedral_angle_4_deg 21.498 r_dihedral_angle_3_deg 14.485 r_lrange_it 9.435 r_dihedral_angle_1_deg 6.449 r_scangle_it 2.579 r_mcangle_it 2.325 r_scbond_it 1.635 r_mcbond_it 1.39 r_angle_refined_deg 1.319 r_nbtor_refined 0.307 r_symmetry_nbd_refined 0.284 r_nbd_refined 0.233 r_symmetry_xyhbond_nbd_refined 0.215 r_metal_ion_refined 0.173 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.1 r_symmetry_metal_ion_refined 0.04 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9412 Nucleic Acid Atoms Solvent Atoms 792 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing