X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529125% w/v PEG-3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, 0.005M activator (from 0.1M stock solution in DMSO)., pH 6.5, vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.549.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.882α = 90
b = 152.564β = 103.17
c = 93.036γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002010-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
11.954099.80.0810.73.6158866
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)
11.951.9897.40.85737719

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 pdb entry 3GQY1.9526.714158798191499.6820.2190.2190.262thin shells (sftools)23.419
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]
-0.709-1.1360.0280.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.075
r_dihedral_angle_4_deg15.671
r_dihedral_angle_3_deg13.272
r_dihedral_angle_1_deg5.71
r_scangle_it3.245
r_scbond_it2.045
r_angle_refined_deg1.425
r_mcangle_it1.284
r_angle_other_deg0.906
r_mcbond_it0.723
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.075
r_dihedral_angle_4_deg15.671
r_dihedral_angle_3_deg13.272
r_dihedral_angle_1_deg5.71
r_scangle_it3.245
r_scbond_it2.045
r_angle_refined_deg1.425
r_mcangle_it1.284
r_angle_other_deg0.906
r_mcbond_it0.723
r_mcbond_other0.18
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15143
Nucleic Acid Atoms
Solvent Atoms675
Heterogen Atoms202

Software

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