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CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 AT 1.35 A RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K4F PDB ENTRY 1K4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.6M AS, 0.1M HEPES, PEG 400, DMSO, PH 7
Crystal Properties Matthews coefficient Solvent content 2.29 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.55 α = 90 b = 96.85 β = 90 c = 125.74 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 CCD 2008-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.35 48.56 96 0.04 27.2 6.1 124977 14.59
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 1.35 1.42 79 0.36 3.3 3
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 1K4F 1.35 48.45 118600 6276 95.93 0.16291 0.16164 0.1584 0.18662 0.1834 RANDOM 18.931
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] -0.2 -0.14 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.765 r_dihedral_angle_4_deg 15.328 r_dihedral_angle_3_deg 13.034 r_sphericity_free 11.623 r_sphericity_bonded 10.021 r_dihedral_angle_1_deg 5.389 r_scangle_it 4.021 r_mcangle_it 3.441 r_scbond_it 2.98 r_mcbond_it 2.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.765 r_dihedral_angle_4_deg 15.328 r_dihedral_angle_3_deg 13.034 r_sphericity_free 11.623 r_sphericity_bonded 10.021 r_dihedral_angle_1_deg 5.389 r_scangle_it 4.021 r_mcangle_it 3.441 r_scbond_it 2.98 r_mcbond_it 2.626 r_rigid_bond_restr 2.09 r_angle_refined_deg 1.531 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.246 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3888 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling AMoRE phasing