X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.929310% PEG 4000, 0.05M sodium acetate, 4% glycerol, 0.1M MES , pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
358.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.01α = 78.71
b = 63.49β = 89.71
c = 74.99γ = 89.91
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARRESEARCHDynamically bendable mirror2008-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.978960SLSX10SA

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
12.54094.80.06117.032626724911-341.374
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)
2.52.75970.2336.7

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 2OIQ2.536.7126267249088721000.2460.2440.295RANDOM12.399
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]
0.75-0.080.48-1.580.090.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.684
r_dihedral_angle_3_deg19.389
r_dihedral_angle_4_deg16.137
r_dihedral_angle_1_deg6.595
r_angle_refined_deg1.738
r_nbtor_refined0.316
r_symmetry_vdw_refined0.261
r_symmetry_hbond_refined0.257
r_nbd_refined0.229
r_xyhbond_nbd_refined0.199
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.684
r_dihedral_angle_3_deg19.389
r_dihedral_angle_4_deg16.137
r_dihedral_angle_1_deg6.595
r_angle_refined_deg1.738
r_nbtor_refined0.316
r_symmetry_vdw_refined0.261
r_symmetry_hbond_refined0.257
r_nbd_refined0.229
r_xyhbond_nbd_refined0.199
r_chiral_restr0.112
r_bond_refined_d0.018
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4189
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms60

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling