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Crystal Structure of the Human CAMKK1A in complex with Hesperadin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZV2 PDB entry 2ZV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 280 33% PEG2000 MME, 0.1 M potassium thiocyanate, 0.1 M CHC buffer, pH 7.5, cryoprotectant: 30% polyethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.49 50.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.215 α = 90 b = 83.174 β = 97.27 c = 80.124 γ = 90
Symmetry Space Group P 1 21 1
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 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
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 2.1 19.87 99.5 0.1 0.124 0.073 0.996 9.8 5.2 37282
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 2.1 2.16 99.8 0.847 1.077 0.656 0.576 1.7 4.7
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 PDB entry 2ZV2 2.1 19.87 35378 1885 99.41 0.21218 0.21049 0.24384 0.2413 RANDOM 34.479
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] -0.78 -2 0.62 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.414 r_dihedral_angle_4_deg 18.59 r_dihedral_angle_3_deg 12.405 r_dihedral_angle_1_deg 5.787 r_long_range_B_refined 5.295 r_long_range_B_other 5.294 r_mcangle_it 3.103 r_mcangle_other 3.103 r_scangle_other 3.094 r_mcbond_it 1.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.414 r_dihedral_angle_4_deg 18.59 r_dihedral_angle_3_deg 12.405 r_dihedral_angle_1_deg 5.787 r_long_range_B_refined 5.295 r_long_range_B_other 5.294 r_mcangle_it 3.103 r_mcangle_other 3.103 r_scangle_other 3.094 r_mcbond_it 1.874 r_mcbond_other 1.874 r_scbond_it 1.873 r_scbond_other 1.861 r_angle_refined_deg 1.276 r_angle_other_deg 0.896 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4023 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing