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Crystal structure of E264A 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, 30% dioxane
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.27 α = 90 b = 91.78 β = 90 c = 116.74 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 2014-11-05 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 2.1 58.37 92.7 0.109 12.6 9.9 21909
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 2.1 2.21 0.26
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 2.1 58.37 20692 1113 92.48 0.21573 0.21274 0.2182 0.27256 0.2716 RANDOM 26.607
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] -2.22 1.03 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.61 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 12.501 r_dihedral_angle_1_deg 6.158 r_long_range_B_refined 5.714 r_long_range_B_other 5.714 r_angle_refined_deg 1.216 r_angle_other_deg 0.708 r_mcangle_it 0.599 r_mcangle_other 0.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.61 r_dihedral_angle_4_deg 17.581 r_dihedral_angle_3_deg 12.501 r_dihedral_angle_1_deg 6.158 r_long_range_B_refined 5.714 r_long_range_B_other 5.714 r_angle_refined_deg 1.216 r_angle_other_deg 0.708 r_mcangle_it 0.599 r_mcangle_other 0.599 r_scangle_other 0.469 r_mcbond_it 0.327 r_mcbond_other 0.327 r_scbond_it 0.273 r_scbond_other 0.27 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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 2915 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing