X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Y9O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.12770.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic and 0.1 M sodium acetate pH 4.5, 0.2 M Magnesium Chloride
Crystal Properties
Matthews coefficientSolvent content
2.5251.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.59α = 90
b = 64.59β = 90
c = 135.73γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.7729.1699.60.0520.0570.0220.99918.86.228763
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)
11.771.8299.90.650.7050.2670.8516.72072

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 REPLACEMENTTHROUGHOUT4Y9O1.7729.1627262142799.480.19940.19770.2318RANDOM32.941
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]
1.081.08-2.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.718
r_dihedral_angle_4_deg20.659
r_dihedral_angle_3_deg12.807
r_dihedral_angle_1_deg5.822
r_mcangle_it3.511
r_mcbond_it2.372
r_mcbond_other2.372
r_angle_refined_deg1.637
r_angle_other_deg1.001
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.718
r_dihedral_angle_4_deg20.659
r_dihedral_angle_3_deg12.807
r_dihedral_angle_1_deg5.822
r_mcangle_it3.511
r_mcbond_it2.372
r_mcbond_other2.372
r_angle_refined_deg1.637
r_angle_other_deg1.001
r_chiral_restr0.089
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2004
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
MOLREPphasing