2YVT

Crystal structure of aq_1956


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1oil batch4.529330% (w/v) PEG 8000, 0.1M acetate, 0.2M Li Sulfate , pH 4.5, oil batch, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.733α = 90
b = 72.733β = 90
c = 90.873γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102007-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B20.97893SPring-8BL26B2

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
11.65099.90.03948103760837232-3
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)
11.61.6699.50.1487.863679

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 1UF31.619.2735321185899.930.171140.169510.20189RANDOM17.818
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.93
r_dihedral_angle_3_deg12.396
r_dihedral_angle_4_deg8.535
r_dihedral_angle_1_deg5.81
r_sphericity_free4.534
r_sphericity_bonded3.065
r_scangle_it2.917
r_mcangle_it2.411
r_scbond_it2.016
r_mcbond_it1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.93
r_dihedral_angle_3_deg12.396
r_dihedral_angle_4_deg8.535
r_dihedral_angle_1_deg5.81
r_sphericity_free4.534
r_sphericity_bonded3.065
r_scangle_it2.917
r_mcangle_it2.411
r_scbond_it2.016
r_mcbond_it1.71
r_rigid_bond_restr1.59
r_angle_refined_deg1.153
r_nbtor_refined0.314
r_symmetry_vdw_refined0.223
r_nbd_refined0.202
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.131
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2103
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms

Software

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