X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4R43 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82920.1M Sodium acetate pH 4.6, 30% PEG 300
Crystal Properties
Matthews coefficientSolvent content
2.9257.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.721α = 90
b = 124.598β = 90
c = 121.302γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMAR scanner 345 mm plate2014-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.60243.598.60.07916.42.924105257.22
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.6022.7393.80.261.952.2

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4r432.60243.4622899120698.670.199770.19740.24419RANDOM45.614
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]
-0.020.04-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.363
r_dihedral_angle_4_deg15.441
r_dihedral_angle_3_deg12.978
r_dihedral_angle_1_deg6.399
r_long_range_B_refined5.178
r_long_range_B_other5.176
r_scangle_other3.452
r_mcangle_it3.314
r_mcangle_other3.314
r_scbond_it2.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.363
r_dihedral_angle_4_deg15.441
r_dihedral_angle_3_deg12.978
r_dihedral_angle_1_deg6.399
r_long_range_B_refined5.178
r_long_range_B_other5.176
r_scangle_other3.452
r_mcangle_it3.314
r_mcangle_other3.314
r_scbond_it2.098
r_scbond_other2.098
r_mcbond_it2.036
r_mcbond_other2.034
r_angle_refined_deg1.312
r_angle_other_deg0.913
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
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 Atoms4562
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing