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Refinement of BMP7 crystal structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMP PDB entry 1BMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 277 20% MPD, 0.1M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.94 68.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.294 α = 90 b = 101.294 β = 90 c = 41.812 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH mirror 2000-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.98 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 25 99.6 0.054 16.9 15770 15770 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.08 99.6 0.333
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 (All) 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 1BMP 2 23.96 14892 14892 795 92.61 0.22873 0.22873 0.22788 0.2415 0.24449 0.2543 RANDOM 35.983
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] -1.29 -0.64 -1.29 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.505 r_scangle_it 6.526 r_dihedral_angle_1_deg 5.157 r_scbond_it 4.093 r_mcangle_it 2.88 r_angle_refined_deg 2.462 r_mcbond_it 1.618 r_angle_other_deg 1.424 r_symmetry_hbond_refined 0.667 r_xyhbond_nbd_refined 0.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.505 r_scangle_it 6.526 r_dihedral_angle_1_deg 5.157 r_scbond_it 4.093 r_mcangle_it 2.88 r_angle_refined_deg 2.462 r_mcbond_it 1.618 r_angle_other_deg 1.424 r_symmetry_hbond_refined 0.667 r_xyhbond_nbd_refined 0.409 r_nbtor_other 0.389 r_symmetry_vdw_refined 0.309 r_nbd_refined 0.306 r_symmetry_vdw_other 0.255 r_nbd_other 0.232 r_chiral_restr 0.156 r_xyhbond_nbd_other 0.12 r_bond_refined_d 0.03 r_gen_planes_refined 0.011 r_gen_planes_other 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 828 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 14
Software Software Software Name Purpose HKL-2000 data collection TRUNCATE data reduction REFMAC refinement HKL-2000 data reduction CCP4 data scaling