X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QT4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.9529160uL of the reservoir solution (100 mM Bis-Tris Propane pH 5.95, 200 mM Li2SO4 and 30% PEG 3350) was pipetted into the wells. The drop volume was 0.5uL, composed of 200 nL of 13.7 mg/mL gonoccocal Pth, 200 nL reservoir solution and 100 nL seed crystals. The plate was sealed quickly and kept in an incubator at 18C and the single crystals appeared in 2-7 days.
Crystal Properties
Matthews coefficientSolvent content
2.6653.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.44α = 90
b = 71.51β = 90
c = 146.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9282DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.8337.492.20.0720.0790.0320.99816.56.33812627.96
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.861002.0420.8410.6691.16.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4QT41.8337.41.3337583191690.930.3360.33450.364138.49
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.7197
f_angle_d0.8816
f_chiral_restr0.0527
f_plane_restr0.0071
f_bond_d0.0056
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2965
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing