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Mouse phosphomannomutase 2 in apo state from crystals with PEG 3350
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 8.5 294 Best crystals appeared after 2-7 days using 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, and 27-30% PEG 3350 as reservoir, in hanging drop 24-well plates, by mixing 2 ul of protein with 2 ul of reservoir solution
Crystal Properties Matthews coefficient Solvent content 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.811 α = 90 b = 71.811 β = 90 c = 355.897 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 6M 2022-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.49 177.95 99.3 0.019 0.999 16.7 19.2 89547 25.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.51 98.2 0.627 0.591 1.3 19.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.49 62.19 1.33 89450 4607 98.94 0.1799 0.1791 0.1796 0.1952 0.1975 34.74
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 5.8941 f_angle_d 0.7102 f_chiral_restr 0.0606 f_plane_restr 0.0058 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3890 Nucleic Acid Atoms Solvent Atoms 618 Heterogen Atoms 24
Software Software Software Name Purpose AutoProcess data processing XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement