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Crystal structure of BlaA-1 APO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 2.24631381 45.2776413
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.45 α = 90 b = 72.647 β = 94.302 c = 43.887 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU HyPix-6000HE X ray optics 2022-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541838
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 28.16 99.9 0.13 0.15 0.072 0.992 9.9 7.6 11023
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 99.9 0.284 0.326 0.155 0.973 7.7
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 28.16 11022 567 99.828 0.161 0.1574 0.1567 0.235 0.2316 22.945
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] 4.457 1.879 -2.379 -2.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.104 r_dihedral_angle_3_deg 15.27 r_dihedral_angle_2_deg 8.902 r_lrange_it 7.448 r_lrange_other 7.148 r_dihedral_angle_1_deg 6.619 r_scangle_it 4.377 r_scangle_other 4.201 r_mcangle_it 2.817 r_mcangle_other 2.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.104 r_dihedral_angle_3_deg 15.27 r_dihedral_angle_2_deg 8.902 r_lrange_it 7.448 r_lrange_other 7.148 r_dihedral_angle_1_deg 6.619 r_scangle_it 4.377 r_scangle_other 4.201 r_mcangle_it 2.817 r_mcangle_other 2.816 r_scbond_it 2.652 r_scbond_other 2.541 r_mcbond_it 1.817 r_mcbond_other 1.817 r_angle_refined_deg 1.427 r_angle_other_deg 0.467 r_symmetry_xyhbond_nbd_refined 0.255 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.217 r_nbd_other 0.203 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.18 r_symmetry_nbtor_other 0.08 r_xyhbond_nbd_other 0.072 r_chiral_restr 0.062 r_symmetry_xyhbond_nbd_other 0.048 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1992 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data collection Aimless data scaling MOLREP phasing