X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429824 - 34% PEG 3350 and 100mM HEPES, at pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.2144.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.48α = 90
b = 119.433β = 105.3
c = 88.166γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
12.1510099.90.1320.1430.05410.3765917
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)
12.152.231000.8190.8950.3590.8466.16598

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 REPLACEMENTTHROUGHOUT3DTB2.1585.0462531331898.520.24350.24120.285RANDOM46.667
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]
-1.19-0.71-2.873.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.051
r_dihedral_angle_3_deg13.264
r_dihedral_angle_4_deg12.486
r_dihedral_angle_1_deg5.975
r_angle_refined_deg1.179
r_angle_other_deg0.874
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.051
r_dihedral_angle_3_deg13.264
r_dihedral_angle_4_deg12.486
r_dihedral_angle_1_deg5.975
r_angle_refined_deg1.179
r_angle_other_deg0.874
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9584
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms92

Software

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