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Crystal structure of the T337M variant of human PGM-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 1.8 M ammonium sulfate, 0.1 M MES, pH 6.5, 0.01 cobalt chloride
Crystal Properties Matthews coefficient Solvent content 3.07 59.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.693 α = 90 b = 171.693 β = 90 c = 99.203 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2018-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00001 ALS 4.2.2
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 2.5 49.57 100 0.098 0.11 0.039 0.999 17.2 13.7 51770 61.99
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 2.5 2.58 100 1.7 1.835 0.688 0.747 1.4 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 5epc 2.5 49.57 1.35 51666 2595 99.9 0.2173 0.2145 0.217 0.2696 0.2685 78.14
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.7692 f_angle_d 0.9035 f_chiral_restr 0.055 f_bond_d 0.0073 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7742 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing