X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3P7I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22900.2 M NaCl, 0.1 M phosphate-citrate buffer pH 4.2 and 20 % PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.0138.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.34α = 90
b = 69.31β = 93.07
c = 66.53γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96861DiamondI24

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
11.9547.9697.20.0810.9947.33.635004
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95298.91.33.7

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 REPLACEMENTTHROUGHOUT3P7I1.9547.9633184180297.010.217620.214990.26654RANDOM42.988
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]
-0.53-0.10.76-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.183
r_dihedral_angle_4_deg21.894
r_dihedral_angle_3_deg15.65
r_long_range_B_refined7.018
r_long_range_B_other7.004
r_dihedral_angle_1_deg6.566
r_scangle_other4.818
r_mcangle_it3.992
r_mcangle_other3.991
r_scbond_it2.965
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.183
r_dihedral_angle_4_deg21.894
r_dihedral_angle_3_deg15.65
r_long_range_B_refined7.018
r_long_range_B_other7.004
r_dihedral_angle_1_deg6.566
r_scangle_other4.818
r_mcangle_it3.992
r_mcangle_other3.991
r_scbond_it2.965
r_scbond_other2.964
r_mcbond_it2.658
r_mcbond_other2.657
r_angle_refined_deg1.477
r_angle_other_deg0.946
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3920
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERmodel building