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Crystal structure of OXA-48 beta-lactamase
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 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.1M HEPES, 10% PEG 4000, 8% 1-BUTANOL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.701 α = 90 b = 107.185 β = 111.04 c = 80.787 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 QUANTUM 4 mirrors 2005-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93400 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 30.514 99 0.1004 5.3 5.8 71756 71756
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.949 99.4 0.176 3.6 5.9
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 1K4F 1.9 30.51 71756 71756 7101 100 0.22315 0.21691 0.2166 0.28618 0.2861 RANDOM 16.906
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.726 r_dihedral_angle_4_deg 17.733 r_dihedral_angle_3_deg 16.962 r_dihedral_angle_1_deg 6.507 r_scangle_it 2.899 r_scbond_it 2.106 r_angle_refined_deg 1.609 r_mcangle_it 1.335 r_mcbond_it 0.855 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.726 r_dihedral_angle_4_deg 17.733 r_dihedral_angle_3_deg 16.962 r_dihedral_angle_1_deg 6.507 r_scangle_it 2.899 r_scbond_it 2.106 r_angle_refined_deg 1.609 r_mcangle_it 1.335 r_mcbond_it 0.855 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.216 r_symmetry_hbond_refined 0.215 r_chiral_restr 0.115 r_bond_refined_d 0.016 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7857 Nucleic Acid Atoms Solvent Atoms 762 Heterogen Atoms 16
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling