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Structure of the central domain (MsrA) of Neisseria meningitidis PilB (oxidized form)
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 4.6 293 1 volume of 30% PEG 4000, 0.2M Ammonium Sulfate,0.1M Na Acetate pH 4.6, mixed with 1 volume of 50mM TRIS HCl, 2mM EDTA pH 8, 10mg/mL protein priorly oxidized, microbatch-under-oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.56984 21.648073
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.5 α = 90 b = 47.6 β = 90 c = 66 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 130 mm 2003-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.89 ESRF BM14
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 1.95 20 99.9 0.069 23.8 9.5 10464 10452 12.5
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 1.95 2.06 100 0.358 6.9 9.7 1496
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 1.95 19.3 10465 10360 513 99 0.193 0.1935 0.218 0.2194 RANDOM 29
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] 2.7 3.08 -5.79
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_scangle_it 3.37 c_mcangle_it 2.56 c_scbond_it 2.08 c_mcbond_it 1.92 c_angle_deg 1.2 c_improper_angle_d 0.65 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1303 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction SCALA data scaling CNS phasing