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Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 0.5000M (NH4)2SO4, 1.0000M Li2SO4, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.679 α = 90 b = 72.679 β = 90 c = 156.974 γ = 90
Symmetry Space Group P 43 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 mirror (vertical focusing) 2009-07-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97917,0.97870 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 2.12 30.029 99.6 0.096 11.7 24676 -3 35.549
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 2.12 2.2 99.2 0.948 1.5
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 2.12 30.029 24610 1256 99.69 0.184 0.181 0.1837 0.231 0.2325 RANDOM 37.954
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] 1.43 1.43 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.495 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_4_deg 11.108 r_scangle_it 6.566 r_dihedral_angle_1_deg 6.427 r_scbond_it 4.916 r_mcangle_it 2.865 r_mcbond_it 1.983 r_angle_refined_deg 1.59 r_angle_other_deg 0.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.495 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_4_deg 11.108 r_scangle_it 6.566 r_dihedral_angle_1_deg 6.427 r_scbond_it 4.916 r_mcangle_it 2.865 r_mcbond_it 1.983 r_angle_refined_deg 1.59 r_angle_other_deg 0.961 r_mcbond_other 0.675 r_nbd_refined 0.25 r_symmetry_vdw_other 0.229 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.209 r_nbd_other 0.199 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.094 r_nbtor_other 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2811 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing