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Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 277 0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 3350, 5% Ethanol
Crystal Properties Matthews coefficient Solvent content 1.99 38.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.09 α = 90 b = 66.005 β = 97.61 c = 45.002 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 PILATUS3 R 200K-A Rigaku VariMax HF 2019-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 50 93.8 0.13 0.161 0.094 9.5 2.7 17848
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 1.96 1.99 82.7 0.485 0.599 0.346 0.758 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 6vzk 1.95 33.92 16929 903 93.27 0.2114 0.2093 0.2139 0.2516 0.254 RANDOM 28.074
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 -0.27 0.57 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.961 r_dihedral_angle_4_deg 14.001 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_1_deg 5.857 r_angle_refined_deg 1.181 r_angle_other_deg 1.094 r_chiral_restr 0.045 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.961 r_dihedral_angle_4_deg 14.001 r_dihedral_angle_3_deg 13.729 r_dihedral_angle_1_deg 5.857 r_angle_refined_deg 1.181 r_angle_other_deg 1.094 r_chiral_restr 0.045 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2234 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 17
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction