X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VE6PDB ENTRY 1VE6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529378mM sodium acetate, 0.44mM EDTA, 2.2%PEG 4000, 0.56% beta-octyl-glucoside, 10% DMSO, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.4α = 90
b = 103.334β = 90
c = 168.224γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IIC2005-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
1219.72689.10.09815.1267288-3
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)
122.153.30.562.75399

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 ENTRY 1VE6219.7266390663906337789.260.183630.183630.181470.22441RANDOM17.716
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]
0.1-0.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.469
r_scangle_it2.617
r_scbond_it1.551
r_angle_refined_deg1.308
r_mcangle_it0.88
r_angle_other_deg0.762
r_mcbond_it0.472
r_symmetry_vdw_other0.259
r_nbd_other0.248
r_symmetry_vdw_refined0.231
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.469
r_scangle_it2.617
r_scbond_it1.551
r_angle_refined_deg1.308
r_mcangle_it0.88
r_angle_other_deg0.762
r_mcbond_it0.472
r_symmetry_vdw_other0.259
r_nbd_other0.248
r_symmetry_vdw_refined0.231
r_symmetry_hbond_refined0.2
r_nbd_refined0.194
r_xyhbond_nbd_refined0.145
r_nbtor_other0.088
r_chiral_restr0.071
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8658
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing