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hKHK-C in complex with BI-9787 (pH 5.5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.1 M ammonium acetate, 17% PEG 10,000, 0.1M BIS-TRIS pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.65 66.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.659 α = 90 b = 83.123 β = 90 c = 146.514 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 EIGER X 16M 2023-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99986 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.31 72.3 94.2 1 11.9 13.7 31148
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.313 2.577 0.7
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.313 72.3 31148 1519 70.3 0.2185 0.2176 0.2353 0.2157 RANDOM 69.66
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] 2.9721 -4.0837 1.1116
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.45 t_omega_torsion 2.6 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4555 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 68
Software Software Software Name Purpose BUSTER refinement Coot model building autoPROC data processing Aimless data scaling