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Protein kinase A sixfold mutant model of Aurora B with inhibitor JNJ-7706621
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CDK PDB ENTRY 1CDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 25mM Tris-HCl, 25mM NaCl, 1.5mM octanoyl-N-methylglucamide, 1mM (5-24)-PKI,12-20% (v/v) methanol, 2-methyl 2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.42 α = 90 b = 74.72 β = 90 c = 80.44 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 CCD ADSC QUANTUM 315r 2009-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.91969 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 43.69 99.8 0.069 0.069 6.2 3.1 44032 43939 21.6
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 1CDK 1.75 35.42 41690 2205 98.2 0.19752 0.1961 0.2168 0.22306 0.2377 RANDOM 24.119
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] -0.01 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.113 r_dihedral_angle_4_deg 17.131 r_dihedral_angle_3_deg 12.842 r_dihedral_angle_1_deg 5.187 r_scangle_it 2.622 r_scbond_it 1.576 r_angle_refined_deg 1.146 r_mcangle_it 0.981 r_mcbond_it 0.529 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.113 r_dihedral_angle_4_deg 17.131 r_dihedral_angle_3_deg 12.842 r_dihedral_angle_1_deg 5.187 r_scangle_it 2.622 r_scbond_it 1.576 r_angle_refined_deg 1.146 r_mcangle_it 0.981 r_mcbond_it 0.529 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3002 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 27
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling