X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherPfDTD-Iodide model (not deposited)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29325% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0439.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.905α = 74.8
b = 53.238β = 75.45
c = 91.092γ = 86.07
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2008-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.215094.70.04213.32.743292
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.212.2981.40.4652.53710

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 REPLACEMENTTHROUGHOUTPfDTD-Iodide model (not deposited)2.215043289218195.330.2260.2220.29RANDOM60.5
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]
-1.890.98-2.11-1.253.222.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.439
r_dihedral_angle_3_deg18.656
r_dihedral_angle_4_deg18.098
r_dihedral_angle_1_deg6.464
r_scangle_it1.868
r_angle_refined_deg1.23
r_mcangle_it1.214
r_scbond_it1.169
r_mcbond_it0.676
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.439
r_dihedral_angle_3_deg18.656
r_dihedral_angle_4_deg18.098
r_dihedral_angle_1_deg6.464
r_scangle_it1.868
r_angle_refined_deg1.23
r_mcangle_it1.214
r_scbond_it1.169
r_mcbond_it0.676
r_nbtor_refined0.309
r_nbd_refined0.203
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.161
r_symmetry_hbond_refined0.137
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7466
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms10

Software

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