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Crystal structure of a putative nitroreductase in complex with fmn (cd3205) from clostridium difficile 630 at 1.35 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.7 277 43.1000% 2-methyl-2,4-pentanediol, 0.1M phosphate-citrate pH 3.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.336 α = 90 b = 109.891 β = 104.84 c = 60.635 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) 2008-11-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162,0.97831,0.97870 SSRL BL11-1
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 1.35 29.988 98.2 0.082 0.082 3.938 3.7 99649 14.166
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 1.35 1.39 81.9 0.496 0.496 1.5 3 6124
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 1.35 29.988 99648 4983 98.22 0.135 0.134 0.1431 0.157 0.1621 RANDOM 18.461
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] -0.4 -0.96 -0.38 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.42 r_dihedral_angle_4_deg 13.771 r_dihedral_angle_3_deg 12.78 r_sphericity_free 7.409 r_dihedral_angle_1_deg 5.547 r_sphericity_bonded 3.701 r_scangle_it 2.876 r_mcangle_it 2.61 r_scbond_it 2.093 r_mcbond_it 1.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.42 r_dihedral_angle_4_deg 13.771 r_dihedral_angle_3_deg 12.78 r_sphericity_free 7.409 r_dihedral_angle_1_deg 5.547 r_sphericity_bonded 3.701 r_scangle_it 2.876 r_mcangle_it 2.61 r_scbond_it 2.093 r_mcbond_it 1.932 r_angle_refined_deg 1.504 r_rigid_bond_restr 1.335 r_mcbond_other 1.026 r_angle_other_deg 0.941 r_symmetry_vdw_refined 0.267 r_symmetry_vdw_other 0.225 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.205 r_nbd_other 0.201 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.089 r_chiral_restr 0.086 r_bond_refined_d 0.015 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 3077 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction