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Structure of the central domain (MsrA) of Neisseria meningitidis PilB (complex with a substrate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BQE PDB ENTRY 3BQE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch-under-oil 9 293 1 volume of 30% PEG 550 MME, 0.1M Bicine pH 9.0, 0.1M NaCl, mixed with 1 volume of 50mM TRIS HCl, 2mM EDTA pH 8, 18mg/mL protein + 200mM AcMet(R,S)SONHMe, microbatch-under-oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.679566 26.766775
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.933 α = 90 b = 50.305 β = 90 c = 66.556 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 MAR CCD 165 mm Bent Mirror 2003-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81 EMBL/DESY, HAMBURG X11
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 2.22 20 97.5 0.078 15.3 4.1 7685 7491 15.7
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 2.24 2.28 99.7 0.265 4.24 4.1
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-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 3BQE 2.24 19.8 7475 7169 694 95.9 0.185 0.1855 0.209 0.2085 RANDOM 25.6
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] 1.08 -0.93 -0.15
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_scangle_it 2.36 c_mcangle_it 2.08 c_scbond_it 1.59 c_mcbond_it 1.33 c_angle_deg 1.2 c_improper_angle_d 0.67 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1341 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 14
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction MAR345 data collection DENZO data reduction SCALEPACK data scaling CNS phasing