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Crystal structure of human PHGDH complexed with Compound 15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 297 27% PEG mme 5000, 180 mM ammonium sulfate, 90 mM MES pH 6.5, 2% glycerol, and 20 mM DL-malic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.649 α = 105.98 b = 112.699 β = 96.2 c = 137.84 γ = 101.42
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 EIGER X 16M 2018-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.93 50 93.3 0.099 0.14 0.099 6.8 1.7 49500
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 2.93 3.03 93.5 0.577 0.816 0.577 0.75 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.93 45.42 47083 2339 92.63 0.2761 0.2742 0.2738 0.3148 0.3117 RANDOM 99.666
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] -4.57 1.38 0.96 4.83 3.94 -3.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_3_deg 22.424 r_dihedral_angle_4_deg 21.801 r_dihedral_angle_1_deg 7.036 r_angle_refined_deg 1.766 r_angle_other_deg 1.217 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_3_deg 22.424 r_dihedral_angle_4_deg 21.801 r_dihedral_angle_1_deg 7.036 r_angle_refined_deg 1.766 r_angle_other_deg 1.217 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17938 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 316
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction