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Lactococcal OppA complexed with bradykinin in the closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2M NaCl, 0.1M Na-Hepes, 20% PEG 6000, pH 7.0, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.175 α = 100.97 b = 58.636 β = 101.12 c = 61.277 γ = 103.02
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 Q4 2007-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 58.321 96.2 0.075 0.075 2 1.9 35303 18131
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 95.7 0.259 0.259 2.7 1.9 2660
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3DRF 2.5 58.32 18131 927 96.22 0.22 0.218 0.2182 0.275 0.2764 RANDOM 38.656
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] -0.05 0.03 0.01 0.07 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.717 r_dihedral_angle_4_deg 14.985 r_dihedral_angle_3_deg 12.35 r_dihedral_angle_1_deg 5.064 r_angle_refined_deg 1.001 r_scangle_it 0.482 r_mcangle_it 0.289 r_scbond_it 0.275 r_mcbond_it 0.157 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.717 r_dihedral_angle_4_deg 14.985 r_dihedral_angle_3_deg 12.35 r_dihedral_angle_1_deg 5.064 r_angle_refined_deg 1.001 r_scangle_it 0.482 r_mcangle_it 0.289 r_scbond_it 0.275 r_mcbond_it 0.157 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4441 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 1
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction