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Crystal structure of a domain of unknown function with a heme oxygenase-like fold (sden_3740) from shewanella denitrificans os217 at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20.0% polyethylene glycol 3350, 0.269M magnesium nitrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.81 α = 90 b = 66 β = 90 c = 84.38 γ = 90
Symmetry Space Group P 21 21 2
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 collimating mirror, toroid focusing mirror 2008-03-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97932,0.97918 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 2.3 29.173 97.6 0.041 12.6 23523 -3 47.797
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 2.3 2.38 88.8 0.433 1.9
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 MAD THROUGHOUT 2.3 29.173 23503 1206 99.36 0.221 0.22 0.2214 0.253 0.2494 RANDOM 42.692
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] 3.08 -1.74 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.655 r_dihedral_angle_4_deg 19.04 r_dihedral_angle_3_deg 11.435 r_dihedral_angle_1_deg 2.884 r_angle_refined_deg 1.34 r_scangle_it 1.028 r_angle_other_deg 1.001 r_mcangle_it 1.001 r_scbond_it 0.7 r_mcbond_it 0.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.655 r_dihedral_angle_4_deg 19.04 r_dihedral_angle_3_deg 11.435 r_dihedral_angle_1_deg 2.884 r_angle_refined_deg 1.34 r_scangle_it 1.028 r_angle_other_deg 1.001 r_mcangle_it 1.001 r_scbond_it 0.7 r_mcbond_it 0.679 r_symmetry_vdw_other 0.264 r_mcbond_other 0.26 r_nbd_refined 0.21 r_nbtor_refined 0.183 r_nbd_other 0.169 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.09 r_nbtor_other 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3555 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing