X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V7YPDB ENTRY 1V7Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52772.0M Ammonium sulfate, 0.1M HEPES-NaOH (pH 7.5), 2% (w/v) PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3863.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.136α = 90
b = 182.779β = 90
c = 181.795γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402009-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU1.0SPring-8BL44XU

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
12.65099.50.13610.492082
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)
12.62.6498.80.3772.22

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1V7Y2.648.7987470460399.350.174720.172810.21094RANDOM31.832
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]
0.690.74-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.358
r_dihedral_angle_4_deg23.762
r_dihedral_angle_3_deg23.214
r_dihedral_angle_1_deg8.318
r_scangle_it5.696
r_scbond_it3.8
r_mcangle_it2.174
r_angle_refined_deg2.126
r_mcbond_it1.287
r_angle_other_deg1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.358
r_dihedral_angle_4_deg23.762
r_dihedral_angle_3_deg23.214
r_dihedral_angle_1_deg8.318
r_scangle_it5.696
r_scbond_it3.8
r_mcangle_it2.174
r_angle_refined_deg2.126
r_mcbond_it1.287
r_angle_other_deg1.08
r_chiral_restr0.134
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15256
Nucleic Acid Atoms
Solvent Atoms1187
Heterogen Atoms190

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling