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Crystal Structure of Kemp Eliminase HG3-shell in unbound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 0.5% v/v Jeffamine ED-2001, 0.1 M HEPES, pH 7, 1.1 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 1.704642 27.8889
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.018 α = 90 b = 67.381 β = 90 c = 72.606 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2022-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115870 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 1.44 36.3 94.4 0.07 0.077 0.04 0.99 15.3 6.19 42653 15.09
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 1.44 1.47 65.7 1.017 1.178 0.571 0.576 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 7K4V 1.44 36.3 1.92 42574 2111 94.34 0.1549 0.1542 0.1538 0.1659 0.164 18.29
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 12.8767 f_angle_d 0.927 f_chiral_restr 0.0722 f_bond_d 0.0077 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2296 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction Aimless data scaling MOLREP phasing