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Human CSNK2A2 bound to a Pyrrolo[2,3-d]pyrimidinyl inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 20% PEG3350, 0.2 M potassium nitrate
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.579 α = 90 b = 59.46 β = 93.64 c = 83.08 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 PIXEL DECTRIS PILATUS 2M 2015-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 82.91 98.3 0.06 13.7 4.7 55567
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 85.5 0.13 5 3.2
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 3OFM 1.5 46 52894 2671 98.17 0.12699 0.12504 0.1254 0.16477 0.1644 RANDOM 20.652
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] -0.02 -0.72 -0.59 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.684 r_dihedral_angle_4_deg 22.359 r_sphericity_free 20.765 r_sphericity_bonded 13.894 r_dihedral_angle_3_deg 12.13 r_dihedral_angle_1_deg 5.833 r_scangle_other 4.364 r_long_range_B_refined 4.322 r_long_range_B_other 4.321 r_scbond_it 4.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.684 r_dihedral_angle_4_deg 22.359 r_sphericity_free 20.765 r_sphericity_bonded 13.894 r_dihedral_angle_3_deg 12.13 r_dihedral_angle_1_deg 5.833 r_scangle_other 4.364 r_long_range_B_refined 4.322 r_long_range_B_other 4.321 r_scbond_it 4.002 r_scbond_other 4.002 r_mcangle_it 3.595 r_mcangle_other 3.595 r_mcbond_it 3.126 r_mcbond_other 3.083 r_rigid_bond_restr 2.002 r_angle_refined_deg 1.399 r_angle_other_deg 1.015 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2728 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing