X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GJL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.5 M potassium dihydrogen phosphate and 20 % w/v PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.5952.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.001α = 95.31
b = 99.911β = 106.23
c = 108.558γ = 91.62
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97833DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.534.16950.0670.99810.71.899971
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.540.3430.67

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 REPLACEMENTTHROUGHOUT2GJL2.534.1694928503894.760.188660.185160.25572RANDOM43.158
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]
0.74-0.29-0.790.39-0.24-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.313
r_dihedral_angle_4_deg22.428
r_dihedral_angle_3_deg17.064
r_long_range_B_refined7.9
r_long_range_B_other7.9
r_dihedral_angle_1_deg7.872
r_scangle_other6.166
r_mcangle_it5.497
r_mcangle_other5.497
r_scbond_it4.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.313
r_dihedral_angle_4_deg22.428
r_dihedral_angle_3_deg17.064
r_long_range_B_refined7.9
r_long_range_B_other7.9
r_dihedral_angle_1_deg7.872
r_scangle_other6.166
r_mcangle_it5.497
r_mcangle_other5.497
r_scbond_it4.27
r_scbond_other4.27
r_mcbond_it3.898
r_mcbond_other3.898
r_angle_refined_deg1.066
r_angle_other_deg0.7
r_chiral_restr0.096
r_gen_planes_refined0.01
r_bond_refined_d0.008
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19289
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms272

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction