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Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B in complex with ADP
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 6.6 277 0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.36 47.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.006 α = 90 b = 65.233 β = 95.26 c = 53.713 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 2020-03-03 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 1.96 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 2.75 44.86 7103 399 92.09 0.2007 0.1972 0.2027 0.2622 0.2627 RANDOM 34.825
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] -1.75 0.33 -1.15 2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.874 r_dihedral_angle_4_deg 16.793 r_dihedral_angle_3_deg 16.577 r_dihedral_angle_1_deg 6.969 r_angle_refined_deg 1.267 r_angle_other_deg 1.112 r_chiral_restr 0.049 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.874 r_dihedral_angle_4_deg 16.793 r_dihedral_angle_3_deg 16.577 r_dihedral_angle_1_deg 6.969 r_angle_refined_deg 1.267 r_angle_other_deg 1.112 r_chiral_restr 0.049 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2253 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction