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Crystal Structure of Pseudomonas aeruginosa OccK7 (OpdD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T24 PDB ENTRY 3T24
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 25% PEG 400, 1M sodium formate, 0.05M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.91 68.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.25 α = 90 b = 111.154 β = 123.25 c = 99.933 γ = 90
Symmetry Space Group C 1 2 1
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 270 2012-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.9764 NSLS X6A
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 3.2 40 99.1 0.136 18 7.7 23348
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 3.2 3.26 98.8 0.889 3.55 7.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3T24 3.166 14.989 1.34 23088 1180 97.85 0.2127 0.2096 0.2228 0.2687 0.2794
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.263 f_angle_d 1.395 f_chiral_restr 0.085 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5912 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling