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Crystal structure of the ACVR1 kinase domain in complex with the imidazo[1,2-b]pyridazine inhibitor K00135
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H9R pdb entry 3h9r
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 1.60M MgSO4; 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.4 48.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.8 α = 90 b = 81.86 β = 90 c = 140.39 γ = 90
Symmetry Space Group C 2 2 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 315 Kirkpatrick Baez bimorph mirror pair 2010-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 2.42 44.73 99.8 0.146 8.1 4.5 13074 13046 37.5
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 2.42 2.55 100 0.75 2 4.7 1858
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3h9r 2.42 39.18 2 13046 12375 671 99.66 0.271 0.22268 0.21952 0.2239 0.27922 0.2784 RANDOM 35.896
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] -2.53 6.58 -4.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.713 r_dihedral_angle_4_deg 17.582 r_dihedral_angle_3_deg 16.158 r_dihedral_angle_1_deg 7.837 r_angle_refined_deg 1.467 r_angle_other_deg 0.793 r_chiral_restr 0.123 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.713 r_dihedral_angle_4_deg 17.582 r_dihedral_angle_3_deg 16.158 r_dihedral_angle_1_deg 7.837 r_angle_refined_deg 1.467 r_angle_other_deg 0.793 r_chiral_restr 0.123 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2306 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 57
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling