X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OTKPDB ENTRY 1OTK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293100 mM PIPES, 5% PEG550 MME, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4148.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.631α = 90
b = 77.631β = 90
c = 300.688γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDRAYONIX MX-3002009-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-1

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
12.137.58699.50.0788.65.854874
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)
12.062.1396.60.4334.25506

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1OTK2.137.58654874278299.770.18970.18780.2248RANDOM36.6476
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]
0.940.94-1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.364
r_dihedral_angle_4_deg20.252
r_dihedral_angle_3_deg14.513
r_dihedral_angle_1_deg4.888
r_scangle_it2.67
r_scbond_it1.637
r_angle_refined_deg1.118
r_mcangle_it0.983
r_mcbond_it0.534
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.364
r_dihedral_angle_4_deg20.252
r_dihedral_angle_3_deg14.513
r_dihedral_angle_1_deg4.888
r_scangle_it2.67
r_scbond_it1.637
r_angle_refined_deg1.118
r_mcangle_it0.983
r_mcbond_it0.534
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6268
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms98

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
HKL-2000data reduction