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Crystal structure of protein DVU1097 from Desulfovibrio vulgaris Hildenborough, Pfam DUF375
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 295 2.0M sodium formate, 0.1M Na acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 4.60
Crystal Properties Matthews coefficient Solvent content 3.62 66.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.48 α = 90 b = 81.48 β = 90 c = 151.17 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 MAR CCD 165 mm SGX-CAT 2006-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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 1.98 50 96.3 0.106 8.3 4.8 55000
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) 1.98 2.07 63.5 0.674 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.95 19.98 31401 1717 0.213 0.21 0.2116 0.273 0.281 RANDOM 49.78
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.64 r_dihedral_angle_3_deg 18.03 r_dihedral_angle_4_deg 17.905 r_dihedral_angle_1_deg 6.598 r_scangle_it 3.949 r_scbond_it 2.285 r_mcangle_it 1.791 r_angle_refined_deg 1.483 r_mcbond_it 0.966 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.64 r_dihedral_angle_3_deg 18.03 r_dihedral_angle_4_deg 17.905 r_dihedral_angle_1_deg 6.598 r_scangle_it 3.949 r_scbond_it 2.285 r_mcangle_it 1.791 r_angle_refined_deg 1.483 r_mcbond_it 0.966 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.167 r_metal_ion_refined 0.114 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 3566 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement SHELX refinement DENZO data reduction PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling SHELXD phasing