X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V9S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.42950.05M MES, 1.5M NH2SO4, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.0860.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.312α = 90
b = 91.312β = 90
c = 266.911γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKUGRAPHITE2006-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0SPring-8BL26B1

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
12.84099.90.0976.36.4286892840058
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.999.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1V9S2.8202868926956144799.010.210.210.229RANDOM53.382
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]
1.651.65-3.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.273
r_dihedral_angle_4_deg20.631
r_dihedral_angle_3_deg15.679
r_scangle_it6.071
r_scbond_it3.571
r_mcangle_it2.195
r_angle_refined_deg1.388
r_mcbond_it1.267
r_dihedral_angle_1_deg1.232
r_nbtor_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.273
r_dihedral_angle_4_deg20.631
r_dihedral_angle_3_deg15.679
r_scangle_it6.071
r_scbond_it3.571
r_mcangle_it2.195
r_angle_refined_deg1.388
r_mcbond_it1.267
r_dihedral_angle_1_deg1.232
r_nbtor_refined0.333
r_symmetry_vdw_refined0.313
r_nbd_refined0.27
r_xyhbond_nbd_refined0.154
r_symmetry_hbond_refined0.139
r_chiral_restr0.095
r_bond_refined_d0.008
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6324
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing