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Crystal structure of bone morphogenetic protein 1 protease domain
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 pH 7.5, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.432 α = 90 b = 57.26 β = 90 c = 68.8 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 1.27 68.79 98.3 0.091 0.078 17.1 6.6 58437 57443 -3 -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) 1.27 1.31 86.3 0.471 0.484 2.9 3.9 4393
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 3EDI 1.27 44.02 58437 57442 2873 98.29 0.146 0.144 0.1452 0.177 0.176 RANDOM 14.322
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] 0.19 0.18 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.203 r_dihedral_angle_4_deg 16.795 r_dihedral_angle_3_deg 13.344 r_dihedral_angle_1_deg 5.649 r_sphericity_free 4.902 r_scangle_it 3.867 r_sphericity_bonded 3.232 r_scbond_it 2.822 r_mcangle_it 2.028 r_rigid_bond_restr 1.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.203 r_dihedral_angle_4_deg 16.795 r_dihedral_angle_3_deg 13.344 r_dihedral_angle_1_deg 5.649 r_sphericity_free 4.902 r_scangle_it 3.867 r_sphericity_bonded 3.232 r_scbond_it 2.822 r_mcangle_it 2.028 r_rigid_bond_restr 1.643 r_mcbond_it 1.43 r_angle_refined_deg 1.375 r_nbtor_refined 0.314 r_nbd_refined 0.293 r_symmetry_vdw_refined 0.231 r_xyhbond_nbd_refined 0.18 r_symmetry_hbond_refined 0.168 r_metal_ion_refined 0.104 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1610 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 5
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction