6FWF

Low resolution structure of Neisseria meningitidis qNOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AYF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5283.15PEG 400, cadmium chloride, magnesium chloride, 2-(N-morpholino)ethanesulfonic acid
Crystal Properties
Matthews coefficientSolvent content
4.4772.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.682α = 90
b = 123.096β = 90
c = 130.845γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2013-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

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
14.253.6499.860.2510.2610.070.9985.514.411511170.75
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
14.24.799.97.6817.9542.0530.26414.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3AYF4.253.641100450999.780.3350.33330.3734RANDOM287.437
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]
7.75-5.94-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.813
r_dihedral_angle_3_deg16.45
r_dihedral_angle_4_deg9.92
r_dihedral_angle_1_deg7.177
r_angle_refined_deg1.282
r_angle_other_deg1.043
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.813
r_dihedral_angle_3_deg16.45
r_dihedral_angle_4_deg9.92
r_dihedral_angle_1_deg7.177
r_angle_refined_deg1.282
r_angle_other_deg1.043
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5674
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms88

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing