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Bromine SAD partially resolves multiple binding modes for PKA inhibitor H-89
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDT PDB ENTRY 1YDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 277 10mg/ml protein, 25mM BisTris/MES pH6.9, 50mM KCl, 1.5mM octanoyl-N-methylglucamide, 1mM Protein kinase inhibitor peptide, 5mM H-89 in MeOH', VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.55 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.73 α = 90 b = 75.18 β = 90 c = 80.33 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) 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 1.73 50 99.3 19.08 4.6 32645
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.2 98 5.68 4.6
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 1YDT 1.95 33.39 30935 1652 99.88 0.19203 0.18983 0.189 0.23395 0.2338 RANDOM 21.91
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 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.666 r_dihedral_angle_4_deg 16.844 r_dihedral_angle_3_deg 14.337 r_dihedral_angle_1_deg 5.444 r_angle_refined_deg 1.382 r_angle_other_deg 0.718 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.666 r_dihedral_angle_4_deg 16.844 r_dihedral_angle_3_deg 14.337 r_dihedral_angle_1_deg 5.444 r_angle_refined_deg 1.382 r_angle_other_deg 0.718 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3015 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 35
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling