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Crystal structure of Mg-ADP-bound SecA from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M6N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 299 5 mM ADP, 5 mM MgCl, 2 M ammonium sulfate, 30% glycerol, 1 mM DTT, 100 mM BES,
pH 7.0, VAPOR DIFFUSION, HANGING DROP at 299K
Crystal Properties Matthews coefficient Solvent content 4.09 69.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.245 α = 90 b = 131.245 β = 90 c = 150.453 γ = 120
Symmetry Space Group P 31 1 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 AREA DETECTOR MARRESEARCH 1997-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID2 0.986 ESRF ID2
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 3 50 99.8 0.074 0.074 20.6 7.2 29711 29652 -3 58.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 99.8 1.38 1484
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS THROUGHOUT 1M6N 3 49.45 2 22730 1105 76.1 0.217 0.217 0.233 0.291 0.3116 RANDOM 106.3
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] -6.77 4.05 -6.77 13.54
RMS Deviations Key Refinement Restraint Deviation c_scbond_it 45.42 c_scangle_it 44.27 c_dihedral_angle_d 22.9 c_mcangle_it 11.7 c_mcbond_it 7.73 c_angle_deg 1.8 c_improper_angle_d 1.68 c_bond_d 0.013 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_scbond_it 45.42 c_scangle_it 44.27 c_dihedral_angle_d 22.9 c_mcangle_it 11.7 c_mcbond_it 7.73 c_angle_deg 1.8 c_improper_angle_d 1.68 c_bond_d 0.013 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6402 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 53
Software Software Software Name Purpose X-PLOR refinement DENZO data reduction SCALEPACK data scaling