X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NTD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72900.2 M MgCl2, 0.1 M Hepes pH 7.0 and 25 % (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
1.9536.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.77α = 90
b = 63.62β = 103.39
c = 73.7γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.95DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.653.4398.20.0620.0380.998133.574222
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)
11.61.6496.80.6030.7150.3790.7173.5

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 REPLACEMENTTHROUGHOUT7NTD1.653.4370544365897.940.17780.17580.2172RANDOM22.754
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]
1.03-0.27-1.130.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.8
r_dihedral_angle_4_deg16.646
r_dihedral_angle_3_deg12.384
r_dihedral_angle_1_deg5.715
r_angle_refined_deg1.434
r_angle_other_deg0.96
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.8
r_dihedral_angle_4_deg16.646
r_dihedral_angle_3_deg12.384
r_dihedral_angle_1_deg5.715
r_angle_refined_deg1.434
r_angle_other_deg0.96
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5088
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms3

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing