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Structure of KHK in complex with compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 17-20% PEG 8000, 100 mM sodium citrate, pH 4.4-4.7, and 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.63 66.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.19 α = 90 b = 85.25 β = 90 c = 139.47 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 PILATUS 6M 2013-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
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 2.8 71.45 98.2 0.999 24.9 6.2 24722
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 2.8 2.95 0.888
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5wbm 2.8 31.42 24649 1254 98.2 0.181 0.179 0.216 0.2152 RANDOM 89.69
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] 12.2611 -6.6369 -5.6242
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.5 t_omega_torsion 3.03 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.5 t_omega_torsion 3.03 t_angle_deg 1.2 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4547 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 70
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction autoPROC data reduction Aimless data scaling PHASER phasing