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Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B12
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 2.91 57.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.74 α = 90 b = 105.74 β = 90 c = 97.61 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 2.55 34.61 98.9 0.062 0.062 10.5 4.22 19967 19967
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 2.55 2.65 90.9 0.499 0.499 2.4 3.31
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 2.6 24.58 19071 18089 981 99.6 0.21569 0.21355 0.2209 0.25409 0.2605 RANDOM 77.54
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] -1.27 -0.63 -1.27 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.496 r_dihedral_angle_3_deg 19.183 r_dihedral_angle_4_deg 18.01 r_dihedral_angle_1_deg 7.85 r_scangle_it 3.249 r_scbond_it 2.135 r_angle_refined_deg 1.9 r_mcangle_it 1.706 r_mcbond_it 0.953 r_nbtor_refined 0.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.496 r_dihedral_angle_3_deg 19.183 r_dihedral_angle_4_deg 18.01 r_dihedral_angle_1_deg 7.85 r_scangle_it 3.249 r_scbond_it 2.135 r_angle_refined_deg 1.9 r_mcangle_it 1.706 r_mcbond_it 0.953 r_nbtor_refined 0.334 r_nbd_refined 0.269 r_symmetry_vdw_refined 0.257 r_xyhbond_nbd_refined 0.218 r_chiral_restr 0.127 r_symmetry_hbond_refined 0.033 r_bond_refined_d 0.015 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 2993 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing