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Crystal structure of human ACVR1 (ALK2) kinase in complex with compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q4U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.5 M Ammonium Sulphate, 0.1 M Sodium Citrate, pH 5.6
Crystal Properties Matthews coefficient Solvent content 1.87 34.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.61 α = 90 b = 66.36 β = 90 c = 162.14 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2016-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.04 20 93 0.148 4.8 2.5 16767
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.15 95.8 0.703 1.2 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.04 20 15959 807 92.03 0.21439 0.2108 0.2171 0.28071 0.2807 RANDOM 39.804
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] -0.03 -0.09 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.366 r_dihedral_angle_4_deg 18.297 r_dihedral_angle_3_deg 16.546 r_long_range_B_refined 8.302 r_long_range_B_other 8.183 r_dihedral_angle_1_deg 6.795 r_scangle_other 3.197 r_mcangle_it 2.901 r_mcangle_other 2.901 r_scbond_it 2.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.366 r_dihedral_angle_4_deg 18.297 r_dihedral_angle_3_deg 16.546 r_long_range_B_refined 8.302 r_long_range_B_other 8.183 r_dihedral_angle_1_deg 6.795 r_scangle_other 3.197 r_mcangle_it 2.901 r_mcangle_other 2.901 r_scbond_it 2.078 r_scbond_other 2.077 r_mcbond_it 1.771 r_mcbond_other 1.77 r_angle_refined_deg 1.61 r_angle_other_deg 1.013 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2389 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing