X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DT7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4298PEG 3350, HEPES pH 7.4, MnCl2, GTP
Crystal Properties
Matthews coefficientSolvent content
2.2244.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.924α = 90
b = 119.252β = 106.92
c = 87.397γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2012-04-19SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
1210098.40.11210.26.680162

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 REPLACEMENTTHROUGHOUT3Dt7229.1380019402198.080.19110.18890.2328RANDOM34.935
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]
0.03-0.040.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.384
r_dihedral_angle_4_deg16.672
r_dihedral_angle_3_deg14.255
r_dihedral_angle_1_deg6.311
r_angle_refined_deg1.295
r_angle_other_deg0.755
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.384
r_dihedral_angle_4_deg16.672
r_dihedral_angle_3_deg14.255
r_dihedral_angle_1_deg6.311
r_angle_refined_deg1.295
r_angle_other_deg0.755
r_chiral_restr0.069
r_bond_refined_d0.008
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 Atoms9647
Nucleic Acid Atoms
Solvent Atoms457
Heterogen Atoms115

Software

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