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
2.9658.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.09α = 78.94
b = 63.53β = 89.37
c = 73.99γ = 90.06
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 X10SA0.980890SLSX10SA

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
12.54097.20.08813.152605225330-336.777
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)
12.52.688.70.3693.6

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 2OIQ2.536.59260522532810141000.2240.2220.281RANDOM21.642
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]
-0.06-0.850.59-1.320.161.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.765
r_dihedral_angle_3_deg19.891
r_dihedral_angle_4_deg17.79
r_dihedral_angle_1_deg6.892
r_scangle_it2.94
r_scbond_it1.908
r_angle_refined_deg1.755
r_mcangle_it1.352
r_mcbond_it0.792
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.765
r_dihedral_angle_3_deg19.891
r_dihedral_angle_4_deg17.79
r_dihedral_angle_1_deg6.892
r_scangle_it2.94
r_scbond_it1.908
r_angle_refined_deg1.755
r_mcangle_it1.352
r_mcbond_it0.792
r_nbtor_refined0.319
r_symmetry_hbond_refined0.3
r_symmetry_vdw_refined0.273
r_nbd_refined0.239
r_xyhbond_nbd_refined0.182
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4191
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms78

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling