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Conformational flexibility within the small domain of human serine racemase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HMK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM Bis-Tris pH 6.5, 15% PEG 3350, 250 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.1 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.2 α = 90 b = 155.74 β = 98.48 c = 85.58 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 PILATUS3 6M 2016-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.89 40.87 99.2 0.071 10.5 3.4 98693
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 1.086 1.5 3.4
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 3HMK 1.89 40.87 98652 4925 99.168 0.174 0.1723 0.1723 0.2158 0.2158 53.157
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] -1.246 0.869 1.593 -0.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.977 r_dihedral_angle_4_deg 20.781 r_dihedral_angle_3_deg 16.436 r_lrange_it 14.358 r_dihedral_angle_1_deg 6.974 r_scangle_it 4.561 r_mcangle_it 4.165 r_scbond_it 3.059 r_mcbond_it 2.662 r_angle_refined_deg 1.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.977 r_dihedral_angle_4_deg 20.781 r_dihedral_angle_3_deg 16.436 r_lrange_it 14.358 r_dihedral_angle_1_deg 6.974 r_scangle_it 4.561 r_mcangle_it 4.165 r_scbond_it 3.059 r_mcbond_it 2.662 r_angle_refined_deg 1.859 r_nbtor_refined 0.314 r_symmetry_nbd_refined 0.285 r_metal_ion_refined 0.244 r_nbd_refined 0.24 r_symmetry_xyhbond_nbd_refined 0.179 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.127 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9302 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHENIX phasing