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CTX-M-64 beta-lactamase S130T clavulanic acid complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 0.1 M HEPES, pH7.4, 25% PEG10000
Crystal Properties Matthews coefficient Solvent content 1.81 32.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.16 α = 90 b = 105.54 β = 101.09 c = 47.59 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 315r 2018-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97917 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.19 46.7 74.8 18.6 6 103975
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.22 1.8 3.1
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 5TWD 1.44 40.86 73647 3816 98.21 0.14916 0.14771 0.1527 0.17778 0.1822 RANDOM 14.832
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] 0.04 0.55 -0.31 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.446 r_dihedral_angle_3_deg 11.883 r_dihedral_angle_4_deg 10.013 r_dihedral_angle_1_deg 6.784 r_long_range_B_refined 4.593 r_long_range_B_other 4.415 r_scangle_other 3.442 r_scbond_it 2.327 r_scbond_other 2.327 r_mcangle_it 2.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.446 r_dihedral_angle_3_deg 11.883 r_dihedral_angle_4_deg 10.013 r_dihedral_angle_1_deg 6.784 r_long_range_B_refined 4.593 r_long_range_B_other 4.415 r_scangle_other 3.442 r_scbond_it 2.327 r_scbond_other 2.327 r_mcangle_it 2.083 r_mcangle_other 2.074 r_angle_refined_deg 1.898 r_angle_other_deg 1.61 r_mcbond_it 1.397 r_mcbond_other 1.379 r_chiral_restr 0.205 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3898 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing