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Crystal structure of Escherichia coli DmsD in space group P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EFP 3EFP(a)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 1.25M Ammonium Sulfate, 11% (v/v) Glycerol, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.5 50.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.275 α = 90 b = 96.221 β = 90 c = 210.243 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300HE DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror. 2011-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.105 CLSI 08B1-1
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 2.12 50 98.4 0.109 12.4 8.6 63206 2 -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 2.12 2.2 94.4 0.981 5.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3EFP(a) 2.5 48.6 107698 59979 3180 94.1 0.23189 0.2298 0.2245 0.27068 0.2627 RANDOM 49.563
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] 4.01 -1.38 -2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.671 r_dihedral_angle_4_deg 14.816 r_dihedral_angle_3_deg 13.168 r_dihedral_angle_1_deg 4.442 r_angle_refined_deg 0.903 r_angle_other_deg 0.71 r_scangle_it 0.611 r_scbond_it 0.366 r_mcangle_it 0.236 r_mcbond_it 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.671 r_dihedral_angle_4_deg 14.816 r_dihedral_angle_3_deg 13.168 r_dihedral_angle_1_deg 4.442 r_angle_refined_deg 0.903 r_angle_other_deg 0.71 r_scangle_it 0.611 r_scbond_it 0.366 r_mcangle_it 0.236 r_mcbond_it 0.122 r_chiral_restr 0.048 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13167 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 282
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MxDC data collection HKL-2000 data reduction PHASES phasing