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Crystal structure analysis of BMP-2 in complex with BMPR-IA variant IA/IB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1REW pdb entry 1REW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 0.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.88 57.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.175 α = 90 b = 104.175 β = 90 c = 100.012 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2005-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.5 31.27 99.9 0.083 0.083 11.2 5.23 21360 21360
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 2.5 2.59 99.9 0.564 0.564 2.8 5.32
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 1REW 2.5 31.27 21290 20259 1097 99.79 0.20682 0.20388 0.2007 0.26259 0.2559 RANDOM 81.516
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] -1.1 -0.55 -1.1 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.72 r_dihedral_angle_3_deg 20.577 r_dihedral_angle_4_deg 18.482 r_dihedral_angle_1_deg 6.772 r_scangle_it 2.5 r_scbond_it 1.634 r_angle_refined_deg 1.567 r_mcangle_it 1.338 r_mcbond_it 0.729 r_symmetry_hbond_refined 0.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.72 r_dihedral_angle_3_deg 20.577 r_dihedral_angle_4_deg 18.482 r_dihedral_angle_1_deg 6.772 r_scangle_it 2.5 r_scbond_it 1.634 r_angle_refined_deg 1.567 r_mcangle_it 1.338 r_mcbond_it 0.729 r_symmetry_hbond_refined 0.396 r_symmetry_vdw_refined 0.345 r_nbtor_refined 0.334 r_nbd_refined 0.275 r_xyhbond_nbd_refined 0.21 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2972 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing