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Crystal structure of Bacillus anthracis str. Ames malate dehydrogenase in closed conformation.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UXJ PDB entry 1uxj
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 20% w/v PEG 3350, 0.2M Na Thiocyanate, 2% w/v Hexandiol, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.181 α = 90 b = 68.377 β = 90 c = 142.919 γ = 90
Symmetry Space Group I 2 2 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 ADSC QUANTUM 315r 2011-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9772 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50 99.9 0.076 0.076 27.8 7 36979 36979 -3 15.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99 0.709 0.709 2.2 4.7 1832
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 (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 1uxj 1.7 39.09 33808 33808 1780 97.07 0.15923 0.15923 0.15721 0.1658 0.19764 0.2048 RANDOM 16.578
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] 0.42 -0.07 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.422 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_3_deg 11.661 r_dihedral_angle_1_deg 6.317 r_angle_refined_deg 1.749 r_angle_other_deg 1.032 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.422 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_3_deg 11.661 r_dihedral_angle_1_deg 6.317 r_angle_refined_deg 1.749 r_angle_other_deg 1.032 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.003 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 2353 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 14
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing MOLREP phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling