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1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TLT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 Protein solution: 0.3M Sodium chloride, 0.01M HEPES (pH 7.5), Screen solution: 0.2M Calcium chloride, 2% Glycerol, 20% PEG 3350, 0.01M NAD, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.521 α = 98.1 b = 69.535 β = 106.97 c = 83.098 γ = 115.73
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 Mirrors 2011-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97855 APS 21-ID-D
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 1.63 30 97.1 0.065 16.7 4.3 155282 155282 -3 22.3
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 1.63 1.66 94.8 0.578 2.75 4.2 7631
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 1TLT 1.63 29.97 146631 146631 7763 97.06 0.15985 0.15985 0.15804 0.1656 0.19457 0.1975 RANDOM 18.689
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] 0.5 1.27 -0.36 1.08 -0.2 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.443 r_dihedral_angle_4_deg 14.647 r_dihedral_angle_3_deg 10.467 r_scangle_it 4.775 r_dihedral_angle_1_deg 4.33 r_scbond_it 2.954 r_mcangle_it 1.794 r_angle_refined_deg 1.351 r_mcbond_it 0.995 r_angle_other_deg 0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.443 r_dihedral_angle_4_deg 14.647 r_dihedral_angle_3_deg 10.467 r_scangle_it 4.775 r_dihedral_angle_1_deg 4.33 r_scbond_it 2.954 r_mcangle_it 1.794 r_angle_refined_deg 1.351 r_mcbond_it 0.995 r_angle_other_deg 0.835 r_mcbond_other 0.316 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9654 Nucleic Acid Atoms Solvent Atoms 1191 Heterogen Atoms 91
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling