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Structure of the class D beta-lactamase OXA-1 in complex with doripenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6K PDB entry 1M6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 10% (v/v) PEG 8000, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 39.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.041 α = 90 b = 71.613 β = 99.18 c = 93.139 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 MARMOSAIC 300 mm CCD 2008-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1 APS 21-ID-D
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 1.4 30 96.6 0.074 13.5 5.1 86546
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 1.4 1.45 88.1 0.293 2.9 7834
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1M6K 1.4 28.29 86509 4326 96.45 0.185 0.184 0.206 0.2205 RANDOM 15.268
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] 0.12 0.25 -0.57 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_dihedral_angle_4_deg 14.722 r_dihedral_angle_3_deg 11.882 r_dihedral_angle_1_deg 5.571 r_scangle_it 3.102 r_scbond_it 1.885 r_angle_refined_deg 1.365 r_mcangle_it 1.23 r_mcbond_it 0.664 r_nbtor_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.853 r_dihedral_angle_4_deg 14.722 r_dihedral_angle_3_deg 11.882 r_dihedral_angle_1_deg 5.571 r_scangle_it 3.102 r_scbond_it 1.885 r_angle_refined_deg 1.365 r_mcangle_it 1.23 r_mcbond_it 0.664 r_nbtor_refined 0.333 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3905 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling