☰ Navigation Tabs
Human phosphomannomutase 2 (PMM2) wild-type co-crystallized with the activator glucose 1,6-bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Drops made by mixing 1 microliter of protein solution and 1 microliter of crystallization deposit solution. Protein solution contained 5 mg/ml protein and 3 mM glucose 1,6-bisphophate in 20 mM Hepes pH 7.5 and 0.2 M NaCl. Crystallization solution contained 0.3-0.4 M MgCl2, 24% PEG3350 and 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.96 α = 90 b = 70.96 β = 90 c = 364.28 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS PILATUS 2M 2018-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
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 3.08 61.45 99.9 0.341 0.35 0.081 0.997 8.4 18.5 10988 54
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 3.08 3.129 100 1.539 0.364 0.784 2.2 18.6
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 7O0C 3.08 61.45 1.34 10983 530 99.87 0.2369 0.2359 0.232 0.2565 0.2557 43.24
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 26.2163 f_angle_d 1.1228 f_chiral_restr 0.0533 f_bond_d 0.0086 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3856 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 25
Software Software Software Name Purpose autoPROC data processing PHENIX refinement Aimless data scaling PHASER phasing