X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V19PDB ENTRY 1V19

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5298VAPOUR-DIFFUSION SITTING DROP, AT 298 K. 10.0 MG/ML OF PROTEIN SOLUTION CONTAINING 5 MM ATP WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 0.35 M AMMONIUM SULFATE AND 0.1 M TRIS-HCL BUFFER, PH 8.5. BEFORE THE DATA COLLECTION THE CRYSTAL WAS SOAKED IN SOLUTION CONTAINING 0.35 M MAGNESIUM CHLORIDE INSTEAD OF AMMONIUM SULFATE. THE CRYOPROTECTANT CONTAINED 33% OF ETHYLENE GLYCOL IN ADDITION TO MAGNESIUM CHLORIDE, BUFFER AND ATP
Crystal Properties
Matthews coefficientSolvent content
2.5450.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.721α = 90
b = 84.721β = 90
c = 321.613γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATE R-AXISV2003-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B1SPring-8BL26B1

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
12.65091.70.0819.932.4136923-0.420.2
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)
12.62.6987.80.2841.78

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 1V192.629.4634007162885.10.17790.17790.2658RANDOM46.2
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]
-0.374-3.61-0.3740.747
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23
c_scangle_it7.23
c_mcangle_it5.78
c_scbond_it5.03
c_mcbond_it3.62
c_angle_deg1.2
c_improper_angle_d0.88
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23
c_scangle_it7.23
c_mcangle_it5.78
c_scbond_it5.03
c_mcbond_it3.62
c_angle_deg1.2
c_improper_angle_d0.88
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9156
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms124

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing