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XChem group deposition -- Crystal Structure of human ACVR1 in complex with XS035133b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SRH 6SRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.258 α = 90 b = 84.773 β = 130.97 c = 88.029 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2020-01-17 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.31 66.46 80.1 0.069 0.075 0.029 0.999 12.9 6.1 126970
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 1.34 1.41 26.3 1.262 1.516 0.82 0.452 3 6025
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 FOURIER SYNTHESIS THROUGHOUT 6SRH 1.31 66.47 120273 6387 74.23 0.1656 0.1646 0.1656 0.1851 0.1857 RANDOM 18.008
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] -0.68 -0.38 -0.07 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.222 r_dihedral_angle_4_deg 18.794 r_dihedral_angle_3_deg 11.721 r_dihedral_angle_1_deg 6.628 r_mcangle_it 2.643 r_angle_refined_deg 1.828 r_mcbond_it 1.737 r_mcbond_other 1.737 r_angle_other_deg 1.513 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.222 r_dihedral_angle_4_deg 18.794 r_dihedral_angle_3_deg 11.721 r_dihedral_angle_1_deg 6.628 r_mcangle_it 2.643 r_angle_refined_deg 1.828 r_mcbond_it 1.737 r_mcbond_other 1.737 r_angle_other_deg 1.513 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4575 Nucleic Acid Atoms Solvent Atoms 802 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing