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Crystal structure of a putative organic hydroperoxide resistance protein with molecule of captopril bound in one of the active sites from Vibrio cholerae O1 biovar eltor str. N16961
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EER PDB ENTRY 3EER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1 M sodium Acetate
0.1 M MES
30% Peg 2000MME
30mM captopril
5mM DTT, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.87 34.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.203 α = 90 b = 76.198 β = 90 c = 79.396 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 QUANTUM 315r mirrors 2009-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.96 40 100 0.87 30 6.8 17357 17357 3 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 1.96 1.99 99.8 0.435 3.5 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3EER 1.96 40 17225 16382 873 99.92 0.17349 0.1708 0.192 0.22697 0.2483 RANDOM 13.992
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] 2.69 -2.27 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.984 r_dihedral_angle_4_deg 21.534 r_dihedral_angle_3_deg 15.635 r_dihedral_angle_1_deg 5.863 r_scangle_it 4.865 r_scbond_it 3.073 r_angle_refined_deg 1.758 r_mcangle_it 1.739 r_mcbond_it 1.025 r_angle_other_deg 0.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.984 r_dihedral_angle_4_deg 21.534 r_dihedral_angle_3_deg 15.635 r_dihedral_angle_1_deg 5.863 r_scangle_it 4.865 r_scbond_it 3.073 r_angle_refined_deg 1.758 r_mcangle_it 1.739 r_mcbond_it 1.025 r_angle_other_deg 0.988 r_mcbond_other 0.338 r_chiral_restr 0.112 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2113 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 14
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing Coot model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling