3BQE

Structure of the central domain (MsrA) of Neisseria meningitidis PilB (reduced form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NWAPDB ENTRY 1NWA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microbatch-under-oil7.52931 volume of 20% PEG 8000, 0.1M Na HEPES pH 7.5, mixed with 1 volume of 50mM TRIS HCl, 2mM EDTA pH 8, 18mg/mL protein, microbatch-under-oil, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.6156223.868227

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.488α = 90
b = 49.183β = 90
c = 66.153γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAC Science DIP-20302000-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
123095.70.05614.32.0410048961411.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0390.20.2693.31.98

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NWA216.5410045934246993.10.1750.203RANDOM22.4
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]
0.673.52-4.18
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.3
c_scangle_it3.87
c_scbond_it2.91
c_mcangle_it1.85
c_mcbond_it1.37
c_angle_deg1.2
c_improper_angle_d0.71
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1357
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
XPRESSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing