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Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 35.0000% Dioxane, 0.001 M flavin mononucleotide (FMN), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 46.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.897 α = 90 b = 63.487 β = 131.11 c = 55.465 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) 2009-02-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97840,0.97883 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 1.5 29.348 96.6 0.052 9.97 3 32401 -3 12.217
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) 1.5 1.55 90.9 0.388 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.5 29.348 32400 1637 99.47 0.141 0.139 0.167 0.1614 RANDOM 15.258
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] -0.39 -0.7 0.05 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.17 r_dihedral_angle_3_deg 12.883 r_dihedral_angle_4_deg 10.705 r_scangle_it 6.186 r_dihedral_angle_1_deg 5.764 r_scbond_it 4.034 r_mcangle_it 2.437 r_mcbond_it 1.865 r_angle_refined_deg 1.54 r_angle_other_deg 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.17 r_dihedral_angle_3_deg 12.883 r_dihedral_angle_4_deg 10.705 r_scangle_it 6.186 r_dihedral_angle_1_deg 5.764 r_scbond_it 4.034 r_mcangle_it 2.437 r_mcbond_it 1.865 r_angle_refined_deg 1.54 r_angle_other_deg 0.959 r_mcbond_other 0.425 r_symmetry_vdw_other 0.255 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.216 r_nbd_other 0.202 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.145 r_nbtor_other 0.088 r_chiral_restr 0.087 r_bond_refined_d 0.016 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 1381 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction