☰ Navigation Tabs
Crystal structure of mannonate dehydratase (target EFI-502209) from caulobacter crescentus cb15 complexed with magnesium and d-mannonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1M AMMONIUM SULFATE, 0.1M TRIS-HCL, PH 8.5, 25% PEG3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.12 41.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.801 α = 90 b = 115.801 β = 90 c = 118.131 γ = 90
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 ADSC QUANTUM 315 MIRRORS 2011-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 50 91 0.082 12 4.1 53061 -5 24.361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.45 2.7 4.2
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 3VCN 2 36.62 46026 1410 90.3 0.15694 0.1557 0.1566 0.19553 0.1974 RANDOM 30.59
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] -5.39 -5.39 10.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.044 r_dihedral_angle_4_deg 16.839 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_1_deg 5.953 r_angle_refined_deg 1.223 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.044 r_dihedral_angle_4_deg 16.839 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_1_deg 5.953 r_angle_refined_deg 1.223 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_scbond_it 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 6312 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 27
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling