X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NT0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.8 M Na dihydrogen phosphate 0.8 M K dihydrogen phosphate 0.1 M Hepes buffer pH 7.5 Cryoprotected in 2 M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2562.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.185α = 90
b = 91.792β = 110.91
c = 153.036γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1APS23-ID-B

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
12.32095.10.1067.83.511955829.1
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)
12.32.3879.60.4542.42.99993

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 REPLACEMENTTHROUGHOUT2NT02.319.94119536602194.830.1780.1750.24RANDOM29.096
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]
-0.070.06-0.090.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.509
r_dihedral_angle_4_deg23.386
r_dihedral_angle_3_deg17.744
r_dihedral_angle_1_deg8.18
r_scangle_it4.083
r_scbond_it2.766
r_angle_refined_deg1.969
r_mcangle_it1.798
r_mcbond_it1.095
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.509
r_dihedral_angle_4_deg23.386
r_dihedral_angle_3_deg17.744
r_dihedral_angle_1_deg8.18
r_scangle_it4.083
r_scbond_it2.766
r_angle_refined_deg1.969
r_mcangle_it1.798
r_mcbond_it1.095
r_nbtor_refined0.311
r_xyhbond_nbd_refined0.236
r_nbd_refined0.223
r_symmetry_vdw_refined0.171
r_symmetry_hbond_refined0.158
r_chiral_restr0.135
r_bond_refined_d0.022
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15720
Nucleic Acid Atoms
Solvent Atoms1344
Heterogen Atoms446

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction