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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 1ZWL PDB ENTRY 1ZWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 285 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 285K, pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.68 73.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.35 α = 90 b = 94.35 β = 90 c = 175.38 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 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 0.8100 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 2.6 35 98.9 0.14 12.35 7.2 25285 24986
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) 2.6 2.69 98.1 0.62 2.64 6.7 2435
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZWL 2.6 34.28 25090 24934 1282 99.4 0.201 0.201 0.199 0.1927 0.237 0.2265 RANDOM 29.112
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] 0.08 0.08 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.757 r_dihedral_angle_3_deg 18.173 r_dihedral_angle_4_deg 15.187 r_dihedral_angle_1_deg 13.488 r_scangle_it 2.483 r_angle_refined_deg 1.808 r_scbond_it 1.463 r_mcangle_it 0.972 r_mcbond_it 0.509 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.757 r_dihedral_angle_3_deg 18.173 r_dihedral_angle_4_deg 15.187 r_dihedral_angle_1_deg 13.488 r_scangle_it 2.483 r_angle_refined_deg 1.808 r_scbond_it 1.463 r_mcangle_it 0.972 r_mcbond_it 0.509 r_nbtor_refined 0.319 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.223 r_chiral_restr 0.176 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.117 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2904 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 118
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction