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Crystal structure of the human CDKL5 kinase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BBM PDB ENTRY 4BBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 15% PEG SMEAR MEDIUM, 0.1M TRIS PH 8.0, 0.075M SODIUM ACETATE, 0.15M SODIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.49 50.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.942 α = 90 b = 65.507 β = 90 c = 102.899 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 2013-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 55.02 99.2 0.07 22.6 12.2 23993 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 2.05 92.9 0.37 4.8 8.9
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 PDB ENTRY 4BBM 2 55.26 23136 1243 99.93 0.17517 0.17382 0.1825 0.20135 0.1862 RANDOM 28.581
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] -14.7 4.05 10.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.526 r_dihedral_angle_4_deg 24.315 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 5.818 r_mcangle_it 2.713 r_scbond_it 1.881 r_mcbond_it 1.631 r_mcbond_other 1.615 r_angle_refined_deg 1.29 r_angle_other_deg 0.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.526 r_dihedral_angle_4_deg 24.315 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 5.818 r_mcangle_it 2.713 r_scbond_it 1.881 r_mcbond_it 1.631 r_mcbond_other 1.615 r_angle_refined_deg 1.29 r_angle_other_deg 0.788 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 2196 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing