X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XYFPDB ENTRY 1XYF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293sodium chloride, dipotassium hydrogen phosphate, sodium dihydrogen phosphate, imidazole, cadmium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.21α = 90
b = 34.747β = 104.2
c = 61.586γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 42004-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0Photon FactoryBL-6A

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
11.850940.09836.17.223141
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)
1.81.86940.3088.672213

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1XYF1.848.622383721951119097.080.195420.192120.25981RANDOM15.126
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.132
r_dihedral_angle_4_deg17.329
r_dihedral_angle_3_deg14.569
r_dihedral_angle_1_deg6.326
r_scangle_it3.306
r_scbond_it2.199
r_mcangle_it1.437
r_angle_refined_deg1.423
r_mcbond_it0.882
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.132
r_dihedral_angle_4_deg17.329
r_dihedral_angle_3_deg14.569
r_dihedral_angle_1_deg6.326
r_scangle_it3.306
r_scbond_it2.199
r_mcangle_it1.437
r_angle_refined_deg1.423
r_mcbond_it0.882
r_nbtor_refined0.306
r_symmetry_hbond_refined0.252
r_symmetry_vdw_refined0.223
r_nbd_refined0.193
r_xyhbond_nbd_refined0.151
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2077
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms81

Software

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