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Crystal structure of the class A extended-spectrum beta-lactamase PER- 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E25 PDB ENTRY 1E25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M HEPES, 1.5 M SODIUM CITRATE BUFFER (PH 7.5).
Crystal Properties Matthews coefficient Solvent content 1.89 34.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.48 α = 90 b = 83.88 β = 103.92 c = 68.944 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 PIXEL DECTRIS PILATUS 6M 2012-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 2.2 41.94 100 0.14 10.5 6.8 23354
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 2.2 2.32 100 0.65 3.1 6.9
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 1E25 2.2 33.46 22125 1199 99.91 0.19676 0.19442 0.1943 0.23969 0.2396 RANDOM 29.24
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] 0.02 -0.01 -0.07 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.435 r_dihedral_angle_4_deg 23.793 r_dihedral_angle_3_deg 15.185 r_dihedral_angle_1_deg 6.34 r_angle_refined_deg 1.619 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.435 r_dihedral_angle_4_deg 23.793 r_dihedral_angle_3_deg 15.185 r_dihedral_angle_1_deg 6.34 r_angle_refined_deg 1.619 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 4255 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing