X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QYT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.6298PIPES-Na 100mM pH 6.6, disodium malonate 8mM, PEG 3350 18%, glycerol 17%
Crystal Properties
Matthews coefficientSolvent content
3.8367.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.748α = 90
b = 158.395β = 90
c = 106.61γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1.14026SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.7501000.1250.1330.04479.332206
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.751000.6360.6760.2260.9058.81593

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 REPLACEMENTTHROUGHOUT3QYT2.749.25532206162899.60.17080.16820.2189RANDOM48.231
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]
-1.06-2.693.75
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded44.879
r_dihedral_angle_2_deg37.307
r_dihedral_angle_3_deg16.98
r_dihedral_angle_4_deg15.564
r_rigid_bond_restr6.245
r_dihedral_angle_1_deg5.419
r_angle_refined_deg1.209
r_angle_other_deg0.933
r_chiral_restr0.063
r_bond_refined_d0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_bonded44.879
r_dihedral_angle_2_deg37.307
r_dihedral_angle_3_deg16.98
r_dihedral_angle_4_deg15.564
r_rigid_bond_restr6.245
r_dihedral_angle_1_deg5.419
r_angle_refined_deg1.209
r_angle_other_deg0.933
r_chiral_restr0.063
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4969
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms39

Software

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