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Crystal structure of putative oxidoreductase (YP_050235.1) from Erwinia carotovora atroseptica SCRI1043 at 1.25 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.33 293 NANODROP, 20.0% PEG 8000, 0.2M Magnesium acetate, 0.1M Sodium cacodylate pH 6.33, VAPOR DIFFUSION, SITTING DROP, temperature 293K 2 VAPOR DIFFUSION, SITTING DROP 7 293 NANODROP, 22.0% PEG 8000, 0.15M Magnesium acetate, 0.1M Sodium cacodylate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.05 α = 90 b = 45.83 β = 116.4 c = 87.97 γ = 90
Symmetry Space Group C 1 2 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 325 mm CCD Flat mirror (vertical focusing) 2007-02-24 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2007-02-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.00000 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837, 0.97945, 0.97927 SSRL BL9-2
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 1.25 47.891 95.4 0.079 12.56 184625 16.288
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 1.25 1.3 89.3 0.503 2.4 18354
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 (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 MAD THROUGHOUT 1.25 47.891 184625 9253 99.35 0.157 0.157 0.156 0.1646 0.179 0.1848 RANDOM 9.215
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] -0.13 -0.12 0.22 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.153 r_dihedral_angle_4_deg 16.649 r_dihedral_angle_3_deg 11.841 r_dihedral_angle_1_deg 6.034 r_scangle_it 5.157 r_scbond_it 3.426 r_mcangle_it 2.161 r_angle_refined_deg 1.617 r_mcbond_it 1.507 r_angle_other_deg 0.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.153 r_dihedral_angle_4_deg 16.649 r_dihedral_angle_3_deg 11.841 r_dihedral_angle_1_deg 6.034 r_scangle_it 5.157 r_scbond_it 3.426 r_mcangle_it 2.161 r_angle_refined_deg 1.617 r_mcbond_it 1.507 r_angle_other_deg 0.973 r_mcbond_other 0.5 r_symmetry_vdw_other 0.235 r_symmetry_hbond_refined 0.207 r_nbd_refined 0.204 r_nbd_other 0.203 r_nbtor_refined 0.187 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.107 r_metal_ion_refined 0.1 r_nbtor_other 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5221 Nucleic Acid Atoms Solvent Atoms 849 Heterogen Atoms 30
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing