☰ Navigation Tabs
Crystal Structure of the R503Q 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 0.1 M Tris/HCl pH:7.5, 1.8 M Ammonium Sulfate, 16mg/mL
Crystal Properties Matthews coefficient Solvent content 3 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.131 α = 90 b = 172.131 β = 90 c = 99.805 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 2016-02-02 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 1.95 60.95 100 0.14 0.038 0.999 15.1 14.3 108994 27.988268727
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 1.95 1.98 99.9 1.902 0.526 0.709 1.5 14
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 1.95000322932 60.8574986762 1.34841398363 108895 5485 99.9770473742 0.171520290168 0.16934233003 0.1708 0.212939082377 0.2143 41.8156901318
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 4.48703862513 f_angle_d 0.81183100948 f_chiral_restr 0.0547047114482 f_bond_d 0.00728551734137 f_plane_restr 0.0054957324971
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8552 Nucleic Acid Atoms Solvent Atoms 949 Heterogen Atoms 122
Software Software Software Name Purpose PHENIX refinement PHENIX phasing SCALA data scaling XDS data reduction