X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YUC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.429820-30% PEG 3350, Bis Tris, 5% glycerol, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2645.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.867α = 90
b = 59.856β = 93.86
c = 73.94γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.96Australian SynchrotronMX2

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
11.873.77294.80.11913.274914149141
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.972.40.7970.7970.8920.3930.95.15452

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 REPLACEMENTTHROUGHOUT1YUC1.843.674912449124248794.770.15810.15810.15580.2023RANDOM19.7988
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]
0.030.16-0.280.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.902
r_dihedral_angle_4_deg19.544
r_dihedral_angle_3_deg13.253
r_dihedral_angle_1_deg5.328
r_angle_refined_deg1.855
r_angle_other_deg0.916
r_chiral_restr0.117
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.902
r_dihedral_angle_4_deg19.544
r_dihedral_angle_3_deg13.253
r_dihedral_angle_1_deg5.328
r_angle_refined_deg1.855
r_angle_other_deg0.916
r_chiral_restr0.117
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4108
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms131

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XSCALEdata scaling