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, 85 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9958.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.055α = 79.06
b = 63.397β = 87.72
c = 74.955γ = 90.08
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARRESEARCHDynamically bendable mirror2008-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000000SLSX10SA

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
12.640940.07713.042338921983-338.29
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)
12.62.792.50.2216.22324

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 2OIQ2.64023389219838801000.2130.210.284RANDOM23.622
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]
0.89-0.340.4-1.090.190.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.203
r_dihedral_angle_3_deg20.607
r_dihedral_angle_4_deg18.744
r_dihedral_angle_1_deg7.443
r_scangle_it3.5
r_scbond_it2.279
r_angle_refined_deg1.893
r_mcangle_it1.573
r_mcbond_it0.927
r_symmetry_vdw_refined0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.203
r_dihedral_angle_3_deg20.607
r_dihedral_angle_4_deg18.744
r_dihedral_angle_1_deg7.443
r_scangle_it3.5
r_scbond_it2.279
r_angle_refined_deg1.893
r_mcangle_it1.573
r_mcbond_it0.927
r_symmetry_vdw_refined0.33
r_nbtor_refined0.325
r_nbd_refined0.245
r_xyhbond_nbd_refined0.203
r_symmetry_hbond_refined0.16
r_chiral_restr0.126
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4143
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms76

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling