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High resolution structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SF3 6SF3, 2HLQ experimental model PDB 2HLQ 6SF3, 2HLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 294.15 14% PEG 3350
0.19 M Ammonium citrate dibasic
0.02 M Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.718 α = 90 b = 47.228 β = 90 c = 250.085 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 PIXEL DECTRIS EIGER2 XE 16M 2019-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.91589 Diamond I04
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 1.48 125.04 100 0.111 0.115 0.032 0.999 11.2 12.7 89787
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 1.48 1.51 99.8 1.85 1.933 0.554 0.59 1.4 11.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6SF3, 2HLQ 1.48 125.04 89655 4383 99.886 0.167 0.1646 0.1645 0.2066 0.2066 33.737
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] -0.651 -0.492 1.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.476 r_rigid_bond_restr 15.342 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_4_deg 12.814 r_scangle_it 10.452 r_scangle_other 10.45 r_scbond_it 10.351 r_scbond_other 10.348 r_lrange_it 9.74 r_lrange_other 9.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.476 r_rigid_bond_restr 15.342 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_4_deg 12.814 r_scangle_it 10.452 r_scangle_other 10.45 r_scbond_it 10.351 r_scbond_other 10.348 r_lrange_it 9.74 r_lrange_other 9.721 r_mcangle_it 7.681 r_mcangle_other 7.68 r_dihedral_angle_1_deg 7.214 r_mcbond_other 7.196 r_mcbond_it 7.194 r_angle_refined_deg 1.871 r_angle_other_deg 1.548 r_symmetry_xyhbond_nbd_refined 0.269 r_nbd_refined 0.229 r_symmetry_nbd_refined 0.224 r_nbd_other 0.204 r_symmetry_nbd_other 0.19 r_ncsr_local_group_2 0.183 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.146 r_ncsr_local_group_1 0.121 r_chiral_restr 0.107 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.015 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 3165 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 6
Software Software Software Name Purpose DIALS data reduction Aimless data scaling PHASER phasing REFMAC refinement