X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VGEPDB ENTRIES 1VGE, 1MVU, AND 1D5I
experimental modelPDB 1MVUPDB ENTRIES 1VGE, 1MVU, AND 1D5I
experimental modelPDB 1D5IPDB ENTRIES 1VGE, 1MVU, AND 1D5I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M cacodylate, pH 6.5, 24% PEG8000, 1 M sodium acetate, 5% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5251.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.77α = 90
b = 135.51β = 90
c = 88.25γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDRIGAKU SATURN 944VARIMAX HF2007-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.93099.40.0626.39.53866438664-327.4
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)
11.91.9595.30.3654.24.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1VGE, 1MVU, AND 1D5I1.915375853758599799.40.20580.20580.204790.24276RANDOM32.9
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]
0.58-0.770.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.257
r_scangle_it23.101
r_scbond_it21.428
r_dihedral_angle_4_deg12.781
r_dihedral_angle_3_deg12.134
r_dihedral_angle_1_deg5.973
r_mcangle_it4.263
r_mcbond_it2.577
r_angle_refined_deg1.059
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.257
r_scangle_it23.101
r_scbond_it21.428
r_dihedral_angle_4_deg12.781
r_dihedral_angle_3_deg12.134
r_dihedral_angle_1_deg5.973
r_mcangle_it4.263
r_mcbond_it2.577
r_angle_refined_deg1.059
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3402
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms5

Software

Software
Software NamePurpose
StructureStudiodata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling