X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HKK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529423% (w/v) polyethylene glycol (PEG) 4000, 300 mM magnesium formate and 100 mM Tris-HCl, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6553.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.189α = 90
b = 105.189β = 90
c = 628.624γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.00DiamondI04

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
1447990.1250.1420.0670.99474.335040
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)
144.2990.5120.5890.2850.7984

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 REPLACEMENTTHROUGHOUT5HKK445.5933246166697.930.33270.3310.3666RANDOM161.472
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]
0.840.420.84-2.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.305
r_dihedral_angle_3_deg11.99
r_dihedral_angle_4_deg11.367
r_dihedral_angle_1_deg4.508
r_angle_refined_deg0.733
r_angle_other_deg0.639
r_chiral_restr0.027
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.305
r_dihedral_angle_3_deg11.99
r_dihedral_angle_4_deg11.367
r_dihedral_angle_1_deg4.508
r_angle_refined_deg0.733
r_angle_other_deg0.639
r_chiral_restr0.027
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23414
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms145

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction