X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F5V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729128% PEG 3,000; 100 mM imidazole pH 7.0; 20% DMSO,25 mM hydroxyquinone
Crystal Properties
Matthews coefficientSolvent content
2.0740.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.985α = 90
b = 52.022β = 134.16
c = 64.77γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442011-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.2546.4697.60.0519.26.3959285
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.3584.90.542.4

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 REPLACEMENTTHROUGHOUT1F5V1.2546.0356273297497.630.12480.12320.1549RANDOM16.149
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]
-0.320.17-1.080.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.773
r_dihedral_angle_4_deg20.026
r_dihedral_angle_3_deg11.315
r_dihedral_angle_1_deg5.829
r_rigid_bond_restr1.799
r_angle_refined_deg1.496
r_angle_other_deg1.197
r_chiral_restr0.101
r_bond_refined_d0.01
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.773
r_dihedral_angle_4_deg20.026
r_dihedral_angle_3_deg11.315
r_dihedral_angle_1_deg5.829
r_rigid_bond_restr1.799
r_angle_refined_deg1.496
r_angle_other_deg1.197
r_chiral_restr0.101
r_bond_refined_d0.01
r_gen_planes_refined0.009
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1875
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing