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Crystal structure of Kemp Eliminase HG3.R5 with bound transition state analog 6-nitrobenzotriazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5RGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293.15 100 mM Tris(OHAc), 1.3 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 1.992777 38.31544
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.414 α = 100.723 b = 50.069 β = 102.703 c = 65.584 γ = 99.299
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 EIGER X 16M 2023-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
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 1.5 48.08 96.4 0.056 0.079 0.056 0.995 12.7 3.3 81699
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 1.5 1.53 0.18 0.255 0.18 0.957 3.3
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 1.5 43.202 81698 4133 96.374 0.105 0.1029 0.1025 0.1423 0.1427 7.793
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] 0.51 -0.289 -0.317 -0.914 0.205 0.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.187 r_dihedral_angle_2_deg 14.173 r_dihedral_angle_3_deg 13.788 r_lrange_it 10.474 r_lrange_other 10.035 r_dihedral_angle_1_deg 6.869 r_scangle_it 5.221 r_scangle_other 5.22 r_scbond_it 3.664 r_scbond_other 3.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.187 r_dihedral_angle_2_deg 14.173 r_dihedral_angle_3_deg 13.788 r_lrange_it 10.474 r_lrange_other 10.035 r_dihedral_angle_1_deg 6.869 r_scangle_it 5.221 r_scangle_other 5.22 r_scbond_it 3.664 r_scbond_other 3.664 r_rigid_bond_restr 3.532 r_mcangle_other 3.357 r_mcangle_it 3.354 r_mcbond_it 2.242 r_mcbond_other 2.226 r_angle_refined_deg 1.667 r_angle_other_deg 0.595 r_symmetry_nbd_refined 0.269 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.215 r_nbd_other 0.202 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.192 r_symmetry_xyhbond_nbd_refined 0.191 r_symmetry_xyhbond_nbd_other 0.188 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4554 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction