☰ Navigation Tabs
Crystal structure of mannonate dehydratase from Escherichia coli strain K12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FVM PDB ENTRY 3FVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 25% PEG 3350, 0.1M Tris-HCl,0.1M magnesium chloride hexahydrate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287.0K
Crystal Properties Matthews coefficient Solvent content 2.74 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.961 α = 90 b = 238.461 β = 90 c = 54.345 γ = 90
Symmetry Space Group P 21 21 2
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 MX-225 CCD 2010-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97916 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 132.27 99.7 92475 92475 3.7 3.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 95.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3FVM 2.3 48.42 3.7 92475 92475 4630 99.78 0.1847 0.1847 0.18291 0.1882 0.21863 0.2244 RANDOM 29.102
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] 1.5 -1.36 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.654 r_dihedral_angle_4_deg 16.496 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.127 r_scangle_it 2.06 r_scbond_it 1.217 r_angle_refined_deg 1.144 r_mcangle_it 0.777 r_mcbond_it 0.402 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.654 r_dihedral_angle_4_deg 16.496 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 6.127 r_scangle_it 2.06 r_scbond_it 1.217 r_angle_refined_deg 1.144 r_mcangle_it 0.777 r_mcbond_it 0.402 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12594 Nucleic Acid Atoms Solvent Atoms 889 Heterogen Atoms 8
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling