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Clavulanic acid biosynthesis oligopeptide binding protein 2 complexed with bradykinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WOL PDB ENTRY 2WOL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.511 α = 90 b = 83.327 β = 95.54 c = 62.38 γ = 90
Symmetry Space Group P 1 21 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 CCD M 2007-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.7 62.1 99.7 0.1 18 3.7 59885 19.2
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 1.7 1.74 99.8 0.44 2.6 3.7
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 PDB ENTRY 2WOL 1.7 62.14 56831 3022 99.75 0.18655 0.18462 0.1829 0.22268 0.2205 RANDOM 18.119
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] -1.06 0.18 1.54 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.159 r_dihedral_angle_4_deg 19.913 r_dihedral_angle_3_deg 12.695 r_dihedral_angle_1_deg 5.674 r_scangle_it 3.803 r_scbond_it 2.354 r_angle_refined_deg 1.464 r_mcangle_it 1.395 r_mcbond_it 0.887 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.159 r_dihedral_angle_4_deg 19.913 r_dihedral_angle_3_deg 12.695 r_dihedral_angle_1_deg 5.674 r_scangle_it 3.803 r_scbond_it 2.354 r_angle_refined_deg 1.464 r_mcangle_it 1.395 r_mcbond_it 0.887 r_nbtor_refined 0.308 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.129 r_symmetry_vdw_refined 0.126 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4359 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing