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Crystal Structure of BMP9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BMP PDB ENTRY 3BMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 296 1-1.2 M Sodium Chloride, 7-10 mM Hexadecyltrimethylammonium Bromide 10 mM Magnesium Chloride, pH 7.5, temperature 296K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.8 67.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.234 α = 90 b = 71.234 β = 90 c = 144.897 γ = 90
Symmetry Space Group I 41 2 2
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 ADSC QUANTUM 315 2004-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.0000 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.32 23.8 0.077 13.5 8346 8142
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.4 0.357 11.3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3BMP 2.33 23.8 8346 7954 392 99.52 0.23254 0.23074 0.226 0.27181 RANDOM 63.434
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] -0.45 -0.45 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.911 r_dihedral_angle_3_deg 17.338 r_dihedral_angle_4_deg 10.867 r_dihedral_angle_1_deg 9.234 r_scangle_it 4.439 r_mcangle_it 4.403 r_scbond_it 3.06 r_mcbond_it 2.465 r_angle_refined_deg 1.866 r_symmetry_hbond_refined 0.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.911 r_dihedral_angle_3_deg 17.338 r_dihedral_angle_4_deg 10.867 r_dihedral_angle_1_deg 9.234 r_scangle_it 4.439 r_mcangle_it 4.403 r_scbond_it 3.06 r_mcbond_it 2.465 r_angle_refined_deg 1.866 r_symmetry_hbond_refined 0.366 r_nbtor_refined 0.306 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.103 r_gen_planes_refined 0.02 r_bond_refined_d 0.017 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 831 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction CCP4 data scaling