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
2.448.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.366α = 90
b = 77.366β = 90
c = 301.412γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.2CCDRAYONIX MX-3002009-11-17MSINGLE 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
12.0342.13399.30.06311.81059960
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)
2.032.194.80.3824.15603

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 1OTK2.0342.13359960302999.140.19720.19540.2299RANDOM49.4133
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]
1.271.27-2.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_4_deg20.168
r_dihedral_angle_3_deg13.715
r_dihedral_angle_1_deg4.802
r_scangle_it3.145
r_scbond_it1.933
r_angle_refined_deg1.148
r_mcangle_it1.148
r_mcbond_it0.606
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_4_deg20.168
r_dihedral_angle_3_deg13.715
r_dihedral_angle_1_deg4.802
r_scangle_it3.145
r_scbond_it1.933
r_angle_refined_deg1.148
r_mcangle_it1.148
r_mcbond_it0.606
r_chiral_restr0.109
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6269
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms84

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
HKL-3000data reduction