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Crystal structure of the human CDKL3 kinase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AGU ENSEMBLE OF PDB ENTRIES 4AGU AND 4AAA experimental model PDB 4AAA ENSEMBLE OF PDB ENTRIES 4AGU AND 4AAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.03M ZN CL, 30% PEG_6000, 5% ETHYLENE GLYCOL, MES PH5.5
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.93 α = 90 b = 63.93 β = 90 c = 163.63 γ = 120
Symmetry Space Group P 31 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 100 CCD ADSC CCD 2012-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.2 54.54 99.9 0.1 10.7 5.2 20446 2
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 2.2 2.27 100 0.63 2.5 2.5
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 ENSEMBLE OF PDB ENTRIES 4AGU AND 4AAA 2.2 45.89 18821 1013 97.1 0.21662 0.21425 0.2231 0.26248 0.2689 RANDOM 55.118
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] 1.27 1.27 1.27 -4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.15 r_dihedral_angle_4_deg 24.066 r_dihedral_angle_3_deg 14.956 r_dihedral_angle_1_deg 6.554 r_mcangle_it 1.823 r_scbond_it 1.763 r_angle_refined_deg 1.51 r_mcbond_it 1.143 r_mcbond_other 1.142 r_angle_other_deg 0.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.15 r_dihedral_angle_4_deg 24.066 r_dihedral_angle_3_deg 14.956 r_dihedral_angle_1_deg 6.554 r_mcangle_it 1.823 r_scbond_it 1.763 r_angle_refined_deg 1.51 r_mcbond_it 1.143 r_mcbond_other 1.142 r_angle_other_deg 0.793 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2319 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing