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Structure of WrbA from Pseudomonas aeruginosa
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, HANGING DROP 6 293 16% PEG 3350, 0.12M MgCl, 0.1M Bis pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.02 58.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.314 α = 90 b = 73.331 β = 90 c = 78.672 γ = 90
Symmetry Space Group P 2 2 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 ADSC QUANTUM 4 2005-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A .9791 NSLS X4A
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 20 99.9 0.073 23.4 6.8 13469 13469 -3
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 2.6 2.69 100 0.35 5.8 7.1 1309
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1YDG 2.6 20 -3 13467 13467 732 99.75 0.22871 0.22871 0.22621 0.2274 0.2731 0.2632 RANDOM 57.118
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] 1.09 1.49 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.025 r_dihedral_angle_4_deg 23.972 r_dihedral_angle_3_deg 16.442 r_dihedral_angle_1_deg 6.215 r_scangle_it 1.941 r_angle_refined_deg 1.271 r_scbond_it 1.151 r_mcangle_it 1.101 r_angle_other_deg 0.778 r_mcbond_it 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.025 r_dihedral_angle_4_deg 23.972 r_dihedral_angle_3_deg 16.442 r_dihedral_angle_1_deg 6.215 r_scangle_it 1.941 r_angle_refined_deg 1.271 r_scbond_it 1.151 r_mcangle_it 1.101 r_angle_other_deg 0.778 r_mcbond_it 0.63 r_nbd_refined 0.229 r_symmetry_vdw_other 0.199 r_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.179 r_nbd_other 0.177 r_symmetry_vdw_refined 0.151 r_symmetry_hbond_refined 0.15 r_nbtor_other 0.086 r_mcbond_other 0.083 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2443 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing