X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DIQPDB entry 2DIQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529825% PEG 3350, 0.2M NaCl, 100 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.565α = 90
b = 45.106β = 90
c = 46.561γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2008-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.54178

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
11.7540910.0725.88475
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)
1.751.8199.80.1725.3887

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 2DIQ1.7540843840490.850.2160.2140.257RANDOM22.187
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]
0.33-0.09-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.811
r_dihedral_angle_4_deg17.42
r_dihedral_angle_3_deg11.145
r_dihedral_angle_1_deg6.289
r_scangle_it4.092
r_scbond_it2.837
r_mcangle_it1.854
r_angle_refined_deg1.633
r_mcbond_it1.11
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.811
r_dihedral_angle_4_deg17.42
r_dihedral_angle_3_deg11.145
r_dihedral_angle_1_deg6.289
r_scangle_it4.092
r_scbond_it2.837
r_mcangle_it1.854
r_angle_refined_deg1.633
r_mcbond_it1.11
r_nbtor_refined0.311
r_nbd_refined0.219
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.145
r_chiral_restr0.135
r_symmetry_hbond_refined0.079
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms688
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASESphasing