X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5THP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.1 M TRIS, 2.65 M Ammonium SULPHATE
Crystal Properties
Matthews coefficientSolvent content
3.564.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.53α = 90
b = 130.53β = 90
c = 250.919γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKUmirrors2010-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU R-AXIS IV1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.15130.53940.1070.1210.05410.94.467910
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)
13.153.3290.20.4160.4160.4720.2141.84

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 REPLACEMENTTHROUGHOUT5THP3.1592.4764376340293.740.21490.21190.2713RANDOM51.751
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]
1.71.7-3.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.934
r_dihedral_angle_4_deg19.026
r_dihedral_angle_3_deg18.939
r_dihedral_angle_1_deg9.709
r_angle_refined_deg1.462
r_angle_other_deg1.188
r_chiral_restr0.05
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.934
r_dihedral_angle_4_deg19.026
r_dihedral_angle_3_deg18.939
r_dihedral_angle_1_deg9.709
r_angle_refined_deg1.462
r_angle_other_deg1.188
r_chiral_restr0.05
r_bond_refined_d0.006
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 Atoms21486
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms97

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing