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Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.58 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 20.0000% 2-propanol, 20.0000% polyethylene glycol 4000, 0.1M citric acid pH 5.6, 0.001 M NADH (Nicotinamide-adenine dinucleotide, reduced), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.369 α = 90 b = 87.924 β = 102.33 c = 87.501 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 collimating mirror, toroid focusing mirror 2009-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.58 29.374 99.6 0.123 0.123 9.5 3.8 117477 14.523
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.62 98.7 0.75 0.75 1.6 3.8 8603
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 1.58 29.374 117448 5893 99.49 0.18 0.178 0.1827 0.218 0.2199 RANDOM 15.995
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] 0.1 0.15 0.23 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.626 r_dihedral_angle_4_deg 14.483 r_dihedral_angle_3_deg 12.074 r_dihedral_angle_1_deg 5.936 r_scangle_it 5.859 r_scbond_it 4.429 r_mcangle_it 2.59 r_mcbond_it 2.159 r_angle_refined_deg 1.594 r_angle_other_deg 1.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.626 r_dihedral_angle_4_deg 14.483 r_dihedral_angle_3_deg 12.074 r_dihedral_angle_1_deg 5.936 r_scangle_it 5.859 r_scbond_it 4.429 r_mcangle_it 2.59 r_mcbond_it 2.159 r_angle_refined_deg 1.594 r_angle_other_deg 1.006 r_mcbond_other 0.58 r_symmetry_vdw_other 0.216 r_nbd_refined 0.215 r_nbd_other 0.207 r_symmetry_hbond_refined 0.188 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.097 r_symmetry_vdw_refined 0.087 r_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5524 Nucleic Acid Atoms Solvent Atoms 875 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction