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Mouse phosphomannomutase 2 in complex 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 291 Drops of 2 ul of protein and 2 mM glucose-1,6-bisphosphate (Sigma) and 2 ul of reservoir solution. Best crystals appeared after 2-7 days in 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, 20-22% PEG 8000. Crystals were cryo-protected by briefly soaking in mother liquor with increasing concentrations of PEG up to 30% and 5% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.285 α = 90 b = 99.138 β = 90 c = 213.47 γ = 90
Symmetry Space Group P 21 21 21
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 2022-04-22 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 2.75 213.47 98 0.097 0.993 6.6 6.6 45273 61.1
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 2.75 2.85 100 0.883 0.558 1 6.6
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 2.75 64.67 1.9 45273 4319 98.81 0.2084 0.2054 0.2166 0.2647 0.2704 65.48
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 5.5907 f_angle_d 0.685 f_chiral_restr 0.0427 f_plane_restr 0.0129 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11503 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 103
Software Software Software Name Purpose AutoProcess data processing PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing