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Lactococcal OppA complexed with an endogenous peptide in the closed conformation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2M NaCl, 0.1M Na-Hepes, pH 7.0, 20% PEG 6000, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 36.430637
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.114 α = 90 b = 74.65 β = 90 c = 115.445 γ = 90
Symmetry Space Group P 21 21 21
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 Q210r 2007-02-18 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC Q315R 2007-02-18 M MAD 3 1 x-ray 100 CCD ADSC Q315R 2007-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.999 ESRF BM16 2 SYNCHROTRON ESRF BEAMLINE ID29 0.9197, 0.9199, 0.9168 ESRF ID29 3 SYNCHROTRON ESRF BEAMLINE ID29 1.775 ESRF ID29
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 1,2,3 1.3 99.4 0.053 19.61 124464 -3 14.587
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) 1,2,3 1.3 1.38 97.9 0.364 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.3 62.75 119254 6300 99.64 0.13286 0.13132 0.1413 0.16147 0.1693 RANDOM 8.442
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] 0.03 -0.2 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.259 r_dihedral_angle_4_deg 16.57 r_dihedral_angle_3_deg 10.93 r_dihedral_angle_1_deg 6.597 r_sphericity_free 4.051 r_scangle_it 3.074 r_scbond_it 2.051 r_sphericity_bonded 1.803 r_mcangle_it 1.381 r_angle_refined_deg 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.259 r_dihedral_angle_4_deg 16.57 r_dihedral_angle_3_deg 10.93 r_dihedral_angle_1_deg 6.597 r_sphericity_free 4.051 r_scangle_it 3.074 r_scbond_it 2.051 r_sphericity_bonded 1.803 r_mcangle_it 1.381 r_angle_refined_deg 1.29 r_rigid_bond_restr 0.879 r_angle_other_deg 0.859 r_mcbond_it 0.859 r_mcbond_other 0.339 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4249 Nucleic Acid Atoms Solvent Atoms 1119 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling SHARP phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction