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Thermococcus kadokarensis phosphomannose isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold alphafold2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 0.2M ammonium phosphate, 0.1M Tris pH 8.5 and 50 % V/V MPD
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.158 α = 90 b = 91.158 β = 90 c = 113.378 γ = 120
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 2021-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.16 64.79 99.2 0.997 7.8 2.2 53371
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.2 98.4 0.661 0.297
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 MOLECULAR REPLACEMENT FREE R-VALUE alphafold2 2.16 64.79 53371 1994 98.13 0.2233 0.2208 0.2365 0.2889 0.26 RANDOM 63.241
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] -14.11 -14.11 28.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.237 r_dihedral_angle_4_deg 26.154 r_dihedral_angle_3_deg 22.697 r_dihedral_angle_1_deg 9.999 r_rigid_bond_restr 9.629 r_angle_refined_deg 2.169 r_angle_other_deg 1.434 r_chiral_restr 0.089 r_bond_refined_d 0.024 r_gen_planes_refined 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.237 r_dihedral_angle_4_deg 26.154 r_dihedral_angle_3_deg 22.697 r_dihedral_angle_1_deg 9.999 r_rigid_bond_restr 9.629 r_angle_refined_deg 2.169 r_angle_other_deg 1.434 r_chiral_restr 0.089 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 r_bond_other_d 0.007 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7118 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction