X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JYYPDB entry 3JYY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52830.1M Tris-HCl, 20% PEG 3350, 0.1M Magnesium formate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.689α = 90
b = 96.064β = 90
c = 102.708γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1250980.09614.63.34252518.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0394.70.3683.832073

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 3JYY2504032740327213097.590.171320.171320.16870.22052RANDOM16.06
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]
-0.22-1.421.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.447
r_dihedral_angle_4_deg15.309
r_dihedral_angle_3_deg13.562
r_dihedral_angle_1_deg5.375
r_scangle_it2.228
r_scbond_it1.375
r_angle_refined_deg1.099
r_mcangle_it0.753
r_mcbond_it0.377
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.447
r_dihedral_angle_4_deg15.309
r_dihedral_angle_3_deg13.562
r_dihedral_angle_1_deg5.375
r_scangle_it2.228
r_scbond_it1.375
r_angle_refined_deg1.099
r_mcangle_it0.753
r_mcbond_it0.377
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4346
Nucleic Acid Atoms
Solvent Atoms716
Heterogen Atoms121

Software

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