☰ Navigation Tabs
Crystal Structure of the R515W missense variant of human PGM1
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 7.5 293 0.1M HEPES 7.5, 0.1M Sodium Chloride, 1.5-1.7M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.99 58.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.33 α = 90 b = 172.33 β = 90 c = 99.37 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 2016-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00003 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 60.93 99.7 0.093 0.025 0.999 20.1 13.6 150294 22.2163099368
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 93.6 1.58 0.561 0.595 1.1 8.5
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 MOLECULAR REPLACEMENT FREE R-VALUE 5EPC 1.75000083769 54.4955309177 0.028742346894 149743 7454 99.9666206031 0.166463873181 0.16518324955 0.1666 0.19087048899 0.1916 32.065293762
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 4.42959414693 f_angle_d 0.782577457852 f_chiral_restr 0.0545048562095 f_bond_d 0.00604287594275 f_plane_restr 0.00526958626906
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8512 Nucleic Acid Atoms Solvent Atoms 1180 Heterogen Atoms 105
Software Software Software Name Purpose XDS data reduction PHENIX refinement SCALA data scaling PHENIX phasing