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The Crystal Structure of human PHGDH from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Bis-Tris pH6.5, 25% PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.16 43.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.101 α = 90 b = 121.638 β = 99.974 c = 59.372 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 S 6M 2020-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 42.486 93.7 0.064 6.4 2.3 19518
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 94.5 0.13 2.2
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 6CWA 2.5 42.486 19516 944 93.584 0.263 0.2607 0.2689 0.3196 0.3247 33.884
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] -4.55 -1.675 10.676 -5.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.217 r_dihedral_angle_3_deg 16.568 r_dihedral_angle_4_deg 14 r_dihedral_angle_1_deg 6.941 r_lrange_it 3.979 r_lrange_other 3.978 r_mcangle_it 2.353 r_mcangle_other 2.353 r_scangle_it 1.778 r_scangle_other 1.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.217 r_dihedral_angle_3_deg 16.568 r_dihedral_angle_4_deg 14 r_dihedral_angle_1_deg 6.941 r_lrange_it 3.979 r_lrange_other 3.978 r_mcangle_it 2.353 r_mcangle_other 2.353 r_scangle_it 1.778 r_scangle_other 1.777 r_mcbond_it 1.403 r_mcbond_other 1.403 r_angle_refined_deg 1.326 r_angle_other_deg 1.114 r_scbond_it 1.066 r_scbond_other 1.066 r_symmetry_xyhbond_nbd_refined 0.194 r_nbd_refined 0.188 r_symmetry_nbd_other 0.178 r_xyhbond_nbd_refined 0.17 r_nbd_other 0.163 r_nbtor_refined 0.143 r_symmetry_nbd_refined 0.141 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.045 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3567 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing