☰ Navigation Tabs
Human serine racemase bound to ATP and malonate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG 3350
230 mM sodium malonate
15 mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 1.97 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.943 α = 90 b = 81.191 β = 90 c = 134.468 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 XE 16M 2018-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.978 Diamond I03
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 1.6 50.1 97.5 0.069 0.079 0.999 9.2 4 76688
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 81 0.577 0.705 0.512 1.3 2.5
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 THROUGHOUT 3L6B 1.6 42.651 75542 3722 96.017 0.194 0.1923 0.1923 0.226 0.2258 21.499
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] -0.556 0.546 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.033 r_dihedral_angle_4_deg 20.212 r_dihedral_angle_3_deg 13.416 r_dihedral_angle_1_deg 6.113 r_lrange_it 5.21 r_scangle_it 1.927 r_mcangle_it 1.689 r_angle_refined_deg 1.326 r_scbond_it 1.168 r_mcbond_it 0.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.033 r_dihedral_angle_4_deg 20.212 r_dihedral_angle_3_deg 13.416 r_dihedral_angle_1_deg 6.113 r_lrange_it 5.21 r_scangle_it 1.927 r_mcangle_it 1.689 r_angle_refined_deg 1.326 r_scbond_it 1.168 r_mcbond_it 0.992 r_nbtor_refined 0.306 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.163 r_symmetry_nbd_refined 0.152 r_chiral_restr 0.095 r_metal_ion_refined 0.008 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4800 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement DIALS data reduction pointless data scaling MOLREP phasing