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Crystal Structure of the Extracellular Domain of the Type II BMP Receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HLR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 0.1M Na Citrate, 15% PEG1500, 0.2M Mg acetate, pH 6.0, vapor diffusion, hanging drop, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.73 29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.588 α = 90 b = 45.078 β = 90 c = 48.162 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 113 CCD ADSC QUANTUM 315 2006-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97946 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.45 27.932 96.7 0.053 0.053 9.7 3.8 13746
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.45 1.53 87.1 0.378 0.378 1.1 3.7 1744
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 2HLR 1.45 22.54 13003 707 96.12 0.1923 0.19017 0.1973 0.23159 0.2361 RANDOM 11.826
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] -0.02 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.858 r_dihedral_angle_4_deg 12.71 r_dihedral_angle_3_deg 11.342 r_dihedral_angle_1_deg 6.77 r_sphericity_free 4.046 r_scangle_it 2.79 r_scbond_it 2.259 r_sphericity_bonded 1.791 r_mcangle_it 1.73 r_rigid_bond_restr 1.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.858 r_dihedral_angle_4_deg 12.71 r_dihedral_angle_3_deg 11.342 r_dihedral_angle_1_deg 6.77 r_sphericity_free 4.046 r_scangle_it 2.79 r_scbond_it 2.259 r_sphericity_bonded 1.791 r_mcangle_it 1.73 r_rigid_bond_restr 1.544 r_angle_refined_deg 1.522 r_mcbond_it 1.411 r_angle_other_deg 0.883 r_mcbond_other 0.345 r_symmetry_vdw_refined 0.247 r_xyhbond_nbd_refined 0.219 r_nbd_refined 0.21 r_symmetry_vdw_other 0.205 r_nbd_other 0.203 r_symmetry_hbond_refined 0.186 r_nbtor_refined 0.18 r_chiral_restr 0.092 r_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 812 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling