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Ensemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AMY PDB entry 2AMY
Crystallization Crystal Properties Matthews coefficient Solvent content 2.6 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.622 α = 90 b = 70.622 β = 90 c = 100.15 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Re-refinement using ensemble model THROUGHOUT PDB entry 2AMY 2.09 30.58 17513 924 99.4 0.207 0.207 0.2366 0.298 0.3223 RANDOM 41.9
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 c_dihedral_angle_d 22 c_scangle_it 2.65 c_mcangle_it 2.22 c_scbond_it 2.04 c_mcbond_it 1.51 c_angle_deg 1.3 c_improper_angle_d 0.81 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1943 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 16
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing