X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OIQPDB ENTRY 2OIQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529310% PEG 20000, 15% glycerol, 85mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0159.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.06α = 78.7
b = 63.69β = 87.02
c = 75.12γ = 89.96
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARRESEARCHDynamically bendable mirror2008-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.004730SLSX10SA

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
12.64098.20.06616.12350723074-339.548
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)
2.62.797.40.275.72506

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2OIQ2.64023507230729231000.2230.2210.277RANDOM17.864
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]
0.66-0.590.2-0.910.240.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.853
r_dihedral_angle_3_deg19.159
r_dihedral_angle_4_deg19.02
r_dihedral_angle_1_deg7.202
r_scangle_it3.31
r_scbond_it2.135
r_angle_refined_deg1.865
r_mcangle_it1.455
r_mcbond_it0.866
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.853
r_dihedral_angle_3_deg19.159
r_dihedral_angle_4_deg19.02
r_dihedral_angle_1_deg7.202
r_scangle_it3.31
r_scbond_it2.135
r_angle_refined_deg1.865
r_mcangle_it1.455
r_mcbond_it0.866
r_nbtor_refined0.321
r_symmetry_vdw_refined0.289
r_nbd_refined0.243
r_xyhbond_nbd_refined0.211
r_symmetry_hbond_refined0.192
r_chiral_restr0.122
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4159
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms76

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling