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Crystal structure of the G121R mutant of human phosphoglucomutase 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, HANGING DROP 293 1.5 M ammonium sulfate with 0.15 lithium sulfate and 0.1 CAPS buffer, pH 10.5
Crystal Properties Matthews coefficient Solvent content 2.97 58.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.98 α = 90 b = 171.98 β = 90 c = 99.9 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 2015-10-25 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) 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 2.35 60.943 99.8 0.123 16.5 14.1 71761 55.3
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 2.35 2.41 99.2 3.101 0.8 12.4
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 FREE R-VALUE 5EPC 2.5 60.943 1.37 71761 4983 99.8 0.1944 0.1918 0.1973 0.2427 0.2466
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 13.288 f_angle_d 1.125 f_chiral_restr 0.046 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8051 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling