X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GNYPDB ENTRY 3GNY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1 M sodium cacodylate trihydrate pH 6.5; 0.2 M sodium citrate tribasic dehydrate; 30% isopropanol , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.146α = 90
b = 30.645β = 90
c = 39.82γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.5630.643980.0590.08120.76.38440823211
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.561.6288.20.1320.14118.86.2737

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 3GNY1.56157837822038397.580.1910.190.208RANDOM12.556
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]
-0.010.16-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.562
r_dihedral_angle_4_deg15.653
r_dihedral_angle_3_deg10.523
r_dihedral_angle_1_deg7.929
r_scangle_it4.186
r_scbond_it2.678
r_angle_refined_deg1.733
r_mcangle_it1.712
r_mcbond_it1.016
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.562
r_dihedral_angle_4_deg15.653
r_dihedral_angle_3_deg10.523
r_dihedral_angle_1_deg7.929
r_scangle_it4.186
r_scbond_it2.678
r_angle_refined_deg1.733
r_mcangle_it1.712
r_mcbond_it1.016
r_chiral_restr0.11
r_bond_refined_d0.015
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms466
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing