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Crystal structure of class A beta-lactamase PSE-4 WT- Apo state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G68
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 2.5 M Ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.25 45.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.951 α = 90 b = 95.951 β = 90 c = 61.509 γ = 90
Symmetry Space Group P 41 21 2
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 RIGAKU HyPix-6000HE X ray Optics 2023-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.4 27.226 98.9 0.153 0.161 0.049 0.999 14.6 19.5 11708
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 1.228 1.292 0.4 0.955 19.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 27.226 11566 573 77.9944 0.213 0.2088 0.1906 0.2719 0.2771 42.031
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] -2.611 -2.611 5.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.918 r_dihedral_angle_3_deg 15.207 r_dihedral_angle_2_deg 11.925 r_lrange_it 9.139 r_lrange_other 9.07 r_dihedral_angle_1_deg 7.335 r_scangle_it 6.786 r_scangle_other 6.235 r_mcangle_it 5.628 r_mcangle_other 5.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.918 r_dihedral_angle_3_deg 15.207 r_dihedral_angle_2_deg 11.925 r_lrange_it 9.139 r_lrange_other 9.07 r_dihedral_angle_1_deg 7.335 r_scangle_it 6.786 r_scangle_other 6.235 r_mcangle_it 5.628 r_mcangle_other 5.626 r_scbond_it 4.703 r_scbond_other 4.149 r_mcbond_it 4.033 r_mcbond_other 4.016 r_angle_refined_deg 1.559 r_angle_other_deg 0.502 r_nbd_refined 0.232 r_symmetry_nbd_refined 0.214 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.182 r_nbd_other 0.17 r_symmetry_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.07 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2038 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection Coot model building Aimless data scaling MOLREP phasing