☰ Navigation Tabs
Crystal structure of bone morphogenetic protein 1 protease domain in complex with partially bound DMSO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EDI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 5% DMSO, pH 7.5, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.499 α = 90 b = 59.093 β = 90 c = 69.451 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 100 CCD MARMOSAIC 225 mm CCD 2007-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
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 1.25 59.09 97.9 0.083 0.066 15.5 6 61581 60273 -3 15.7
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) 1.25 1.29 96.1 0.394 0.5 3.66 5.75 5271
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 3EDI 1.25 44.99 60271 3014 97.88 0.142 0.14 0.1395 0.172 0.1725 RANDOM 15.07
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] 0.57 -0.39 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.53 r_dihedral_angle_4_deg 15.808 r_dihedral_angle_3_deg 13.396 r_sphericity_free 6.683 r_dihedral_angle_1_deg 6.418 r_sphericity_bonded 4.36 r_scangle_it 4.119 r_scbond_it 3.038 r_mcangle_it 2.38 r_rigid_bond_restr 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.53 r_dihedral_angle_4_deg 15.808 r_dihedral_angle_3_deg 13.396 r_sphericity_free 6.683 r_dihedral_angle_1_deg 6.418 r_sphericity_bonded 4.36 r_scangle_it 4.119 r_scbond_it 3.038 r_mcangle_it 2.38 r_rigid_bond_restr 1.74 r_mcbond_it 1.627 r_angle_refined_deg 1.578 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.313 r_nbd_refined 0.309 r_xyhbond_nbd_refined 0.212 r_symmetry_hbond_refined 0.183 r_metal_ion_refined 0.124 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1693 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 29
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction