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Crystal structure of a dinb family member protein (sden_0562) from shewanella denitrificans at 1.83 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 NANODROP, 0.271M Ammonium formate, 18.5% Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.437 α = 90 b = 71.722 β = 107.35 c = 93.489 γ = 90
Symmetry Space Group P 1 21 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) 2007-01-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97908, 0.97874 SSRL BL11-1
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 1.83 45.22 92.9 0.065 8.61 68483 31.626
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 1.83 1.9 83.2 0.467 2.2 6155
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 1.83 45.22 68463 3437 98.4 0.159 0.159 0.157 0.164 0.196 0.2004 RANDOM 24.558
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] -0.79 -2.01 -0.3 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_4_deg 21.231 r_dihedral_angle_3_deg 13.141 r_scangle_it 6.534 r_dihedral_angle_1_deg 4.867 r_scbond_it 4.857 r_mcangle_it 2.761 r_mcbond_it 2.002 r_angle_refined_deg 1.492 r_angle_other_deg 1.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.015 r_dihedral_angle_4_deg 21.231 r_dihedral_angle_3_deg 13.141 r_scangle_it 6.534 r_dihedral_angle_1_deg 4.867 r_scbond_it 4.857 r_mcangle_it 2.761 r_mcbond_it 2.002 r_angle_refined_deg 1.492 r_angle_other_deg 1.089 r_mcbond_other 0.84 r_symmetry_vdw_other 0.279 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.227 r_nbtor_refined 0.192 r_nbd_other 0.188 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.094 r_nbtor_other 0.091 r_bond_refined_d 0.018 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5581 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 141
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