X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AF3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2 M sodium chloride, 25% PEG3350, 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.1141.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.65α = 90
b = 72.48β = 90
c = 83.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 R CdTe 300K2013-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9796DiamondI04

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
11.7556.6597.10.10.9959.85.434077
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.7877.30.7092.14.1

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 REPLACEMENTTHROUGHOUT4AF31.7554.6132319171296.710.17850.176480.21626RANDOM18.932
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]
-2.052.91-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.765
r_dihedral_angle_4_deg19.839
r_dihedral_angle_3_deg13.112
r_dihedral_angle_1_deg6.614
r_long_range_B_refined5.287
r_long_range_B_other5.286
r_scangle_other3.004
r_mcangle_other2.275
r_mcangle_it2.272
r_scbond_it1.844
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.765
r_dihedral_angle_4_deg19.839
r_dihedral_angle_3_deg13.112
r_dihedral_angle_1_deg6.614
r_long_range_B_refined5.287
r_long_range_B_other5.286
r_scangle_other3.004
r_mcangle_other2.275
r_mcangle_it2.272
r_scbond_it1.844
r_scbond_other1.843
r_mcbond_it1.397
r_mcbond_other1.391
r_angle_refined_deg1.35
r_angle_other_deg0.894
r_chiral_restr0.219
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2768
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing