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2.17 Angstrom resolution crystal structure of malate dehydrogenase from Vibrio vulnificus CMCP6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 295 Protein: 3.3 mg/mL. Crystallization conditions: 30%PEG 8K, 0.2M Na Acetate , 0.1M Bis-Tris pH 7.0. , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.04 α = 90 b = 80.76 β = 109.42 c = 99.43 γ = 90
Symmetry Space Group P 1 21 1
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 300 mm CCD BE-LENSES 2012-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.17 30 99.9 0.114 13.87 5.3 62995 -3
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 2.17 2.21 99.9 0.679 2.19 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HHP 2.17 29.2 59311 59311 3147 99.8 0.165 0.163 0.207 0.1988 RANDOM 34.21
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] 1.34 -0.74 -0.64 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.108 r_dihedral_angle_4_deg 8.748 r_dihedral_angle_3_deg 7.607 r_scangle_it 2.719 r_dihedral_angle_1_deg 1.645 r_scbond_it 1.629 r_angle_refined_deg 1.27 r_mcangle_it 0.91 r_angle_other_deg 0.796 r_mcbond_it 0.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.108 r_dihedral_angle_4_deg 8.748 r_dihedral_angle_3_deg 7.607 r_scangle_it 2.719 r_dihedral_angle_1_deg 1.645 r_scbond_it 1.629 r_angle_refined_deg 1.27 r_mcangle_it 0.91 r_angle_other_deg 0.796 r_mcbond_it 0.487 r_mcbond_other 0.109 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8875 Nucleic Acid Atoms Solvent Atoms 709 Heterogen Atoms 16
Software Software Software Name Purpose Blu-Ice data collection mrbump/molrep model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MRBUMP/MOLREP phasing