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Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B1
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 57.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.961 α = 90 b = 105.961 β = 90 c = 96.789 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 CCD MARMOSAIC 225 mm CCD 2005-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9796 BESSY 14.1
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 2.44 34.68 99.2 0.046 0.046 13.8 4.11 22783 22783
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 2.44 2.53 93.2 0.339 0.339 3.3 3.2
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 2.44 30.59 23743 21585 1160 99.05 0.19976 0.19706 0.2021 0.25338 0.2571 RANDOM 87.859
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.597 r_dihedral_angle_4_deg 22.858 r_dihedral_angle_3_deg 19.068 r_dihedral_angle_1_deg 6.457 r_scangle_it 2.783 r_scbond_it 1.816 r_angle_refined_deg 1.535 r_mcangle_it 1.503 r_mcbond_it 0.835 r_symmetry_hbond_refined 0.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.597 r_dihedral_angle_4_deg 22.858 r_dihedral_angle_3_deg 19.068 r_dihedral_angle_1_deg 6.457 r_scangle_it 2.783 r_scbond_it 1.816 r_angle_refined_deg 1.535 r_mcangle_it 1.503 r_mcbond_it 0.835 r_symmetry_hbond_refined 0.352 r_nbtor_refined 0.328 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.25 r_xyhbond_nbd_refined 0.218 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 3008 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing