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Crystal Structure of Kemp Eliminase HG649 with bound transition state analogue, 280 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other HG630 280 Crystallographic model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 12.5 mg/mL protein, 30% PEG4000, 0.3 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.072 α = 90 b = 77.465 β = 105.276 c = 93.811 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 280 PIXEL DECTRIS PILATUS3 6M 2023-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
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 1.45 90.5 99.7 0.092 0.11 0.059 0.996 8.7 3.2 124369 12.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 99.7 0.837 0.552 0.452 1 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.45 90.5 1.38 124320 6289 99.69 0.1383 0.1373 0.1383 0.1567 0.1575 19.77
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.6976 f_angle_d 0.8853 f_chiral_restr 0.0711 f_bond_d 0.007 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4574 Nucleic Acid Atoms Solvent Atoms 670 Heterogen Atoms 24
Software Software Software Name Purpose xia2 data reduction DIALS data reduction Aimless data scaling Coot model building PHASER phasing PHENIX refinement