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WrbA from Escherichia coli, native structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDG PDB entry 1YDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 15-35 % PEG 1500, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.68 73.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.361 α = 90 b = 94.361 β = 90 c = 175.363 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 MARRESEARCH mirrors 2006-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.0 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.66 50 98.7 0.12 12.1 6.3 92983 91774 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 97.3 0.68 2.2 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YDG 1.66 29.41 2 89229 86954 4609 97.45 0.16988 0.16902 0.1682 0.18573 0.1837 RANDOM 29.749
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] 0.04 0.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.145 r_dihedral_angle_4_deg 15.26 r_dihedral_angle_3_deg 12.9 r_dihedral_angle_1_deg 5.397 r_scangle_it 3.137 r_scbond_it 1.954 r_angle_refined_deg 1.328 r_mcangle_it 1.161 r_mcbond_it 0.742 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.145 r_dihedral_angle_4_deg 15.26 r_dihedral_angle_3_deg 12.9 r_dihedral_angle_1_deg 5.397 r_scangle_it 3.137 r_scbond_it 1.954 r_angle_refined_deg 1.328 r_mcangle_it 1.161 r_mcbond_it 0.742 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.261 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2916 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing