X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GQYisomorphous replacement with pdb entry 3GQY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29120% PEG3350, 0.2M diammonium tartrate, 0.005M activator, 0.005M ADP, vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3547.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.275α = 90
b = 153.206β = 102.91
c = 93.138γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97934CLSI08ID-1

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
11.65096.30.05910.23.6283418
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)
1.61.6675.20.7072.522112

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 DIFFRACTIONTHROUGHOUTisomorphous replacement with pdb entry 3GQY1.630280370291696.2730.2080.2080.231thin shells (sftools)20.294
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]
-0.546-0.94-0.0110.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.875
r_dihedral_angle_4_deg15.465
r_dihedral_angle_3_deg11.864
r_dihedral_angle_1_deg5.375
r_scangle_it2.803
r_mcangle_it2.239
r_scbond_it1.802
r_mcbond_it1.483
r_angle_refined_deg1.348
r_angle_other_deg0.889
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.875
r_dihedral_angle_4_deg15.465
r_dihedral_angle_3_deg11.864
r_dihedral_angle_1_deg5.375
r_scangle_it2.803
r_mcangle_it2.239
r_scbond_it1.802
r_mcbond_it1.483
r_angle_refined_deg1.348
r_angle_other_deg0.889
r_mcbond_other0.434
r_chiral_restr0.079
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15294
Nucleic Acid Atoms
Solvent Atoms917
Heterogen Atoms292

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MolProbitymodel building
prodrgrefinement