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Crystal structure of human KDM5B in complex with compound 16a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 100 nL of protein is mixed with 200 nL of crystallisation solution containing 1.6 M Na/K phosphate, 0.1 M HEPES pH 7.5, and with 20 nL of seeds obtained in the same conditions. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Crystal Properties Matthews coefficient Solvent content 4.19 70.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.48 α = 90 b = 144.48 β = 90 c = 154.35 γ = 120
Symmetry Space Group P 65 2 2
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-F 2015-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 77.18 99.7 0.113 0.999 21 19.6 42633 56.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 96.5 1.738 0.656 1.8 19.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5a1f 2.3 65.69 42583 2136 99.7 0.188 0.186 0.1905 0.211 0.2132 RANDOM 60.51
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] -3.3396 -3.3396 6.6793
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.35 t_omega_torsion 2.87 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.35 t_omega_torsion 2.87 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 3611 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 127
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing