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Crystal structure of K86A mutant of phosphomannose isomerase from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.8 298 0.1 M Magnesium acetate tetrahydrate, 0.2 M Sodium cacodylate pH 6.8, 20% PEG 8000,5% dioxane
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.19 α = 90 b = 91.73 β = 90 c = 116.66 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 CCD MARMOSAIC 225 mm CCD 2015-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.7 30.58 99.9 0.09 16.3 7.8 43702
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 0.55
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 THROUGHOUT 3H1M 1.7 30.58 41443 2195 99.84 0.1663 0.1642 0.1755 0.20569 0.2133 RANDOM 19.016
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] -0.2 -0.7 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.384 r_dihedral_angle_4_deg 17.709 r_dihedral_angle_3_deg 11.842 r_dihedral_angle_1_deg 6.634 r_long_range_B_other 6.033 r_long_range_B_refined 6.032 r_scangle_other 3.652 r_mcangle_other 2.701 r_mcangle_it 2.7 r_scbond_it 2.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.384 r_dihedral_angle_4_deg 17.709 r_dihedral_angle_3_deg 11.842 r_dihedral_angle_1_deg 6.634 r_long_range_B_other 6.033 r_long_range_B_refined 6.032 r_scangle_other 3.652 r_mcangle_other 2.701 r_mcangle_it 2.7 r_scbond_it 2.414 r_scbond_other 2.411 r_angle_refined_deg 1.918 r_mcbond_it 1.841 r_mcbond_other 1.835 r_angle_other_deg 0.907 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2944 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing