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Crystal structure of E. coli WrbA in complex with FMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R96 PDB ID 2R96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 285 20% PEG 8000, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 1.88 34.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.13 α = 90 b = 61.13 β = 90 c = 168.38 γ = 90
Symmetry Space Group P 41 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 MAR CCD 165 mm mirrors 2006-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, HAMBURG X13
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 1.99 35 90.8 0.09 16.94 6.9 22872 20763
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) 1.99 2.04 84.1 0.51 3.42 6.5 1257
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID 2R96 2 34.67 22461 20367 1034 90.7 0.197 0.197 0.193 0.259 0.2713 RANDOM 22.755
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.628 r_dihedral_angle_3_deg 17.298 r_dihedral_angle_4_deg 16.362 r_dihedral_angle_1_deg 7.101 r_scangle_it 2.901 r_angle_other_deg 2.066 r_scbond_it 1.94 r_angle_refined_deg 1.64 r_mcangle_it 1.343 r_mcbond_it 0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.628 r_dihedral_angle_3_deg 17.298 r_dihedral_angle_4_deg 16.362 r_dihedral_angle_1_deg 7.101 r_scangle_it 2.901 r_angle_other_deg 2.066 r_scbond_it 1.94 r_angle_refined_deg 1.64 r_mcangle_it 1.343 r_mcbond_it 0.844 r_symmetry_hbond_refined 0.327 r_nbtor_refined 0.308 r_nbd_other 0.261 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.222 r_nbtor_other 0.187 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.13 r_mcbond_other 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2873 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction