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Crystal structure of BluB-like flavoprotein (YP_001089088.1) from CLOSTRIDIUM DIFFICILE 630 at 1.74 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 15.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.843 α = 90 b = 183.265 β = 104.89 c = 74.393 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 2008-08-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97918,0.97934 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 1.74 48.337 97.8 0.12 8.64 133857 -3 14.167
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 1.74 1.8 96.8 0.711 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 1.74 48.337 133813 6747 97.86 0.159 0.156 0.1706 0.198 0.2049 RANDOM 27.441
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] 0.55 -1.2 -0.55 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.76 r_dihedral_angle_4_deg 12.759 r_dihedral_angle_3_deg 12.347 r_dihedral_angle_1_deg 5.51 r_scangle_it 2.86 r_scbond_it 1.965 r_angle_refined_deg 1.334 r_mcangle_it 1.061 r_angle_other_deg 0.898 r_mcbond_it 0.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.76 r_dihedral_angle_4_deg 12.759 r_dihedral_angle_3_deg 12.347 r_dihedral_angle_1_deg 5.51 r_scangle_it 2.86 r_scbond_it 1.965 r_angle_refined_deg 1.334 r_mcangle_it 1.061 r_angle_other_deg 0.898 r_mcbond_it 0.767 r_symmetry_vdw_other 0.24 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.225 r_mcbond_other 0.206 r_nbd_other 0.19 r_nbtor_refined 0.187 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.155 r_nbtor_other 0.087 r_chiral_restr 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10336 Nucleic Acid Atoms Solvent Atoms 2045 Heterogen Atoms 282
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction