X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OK7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microbatch with permeable oil5.429320% isopropanol, 20% PEG 4000, 0.1M citrate-NaOH, 2mM 2'P-AMP(Cocrystallization), pH 5.4, Microbatch with permeable oil, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.243α = 90
b = 124.243β = 90
c = 134.255γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.183.9181000.1149.93.1117739117739
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)
2.22.321000.5641.83.117208

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2OK72.262.12111762111762589499.980.258790.258790.25620.30797RANDOM35.724
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]
1.880.941.88-2.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.641
r_dihedral_angle_4_deg19.146
r_dihedral_angle_3_deg15.32
r_dihedral_angle_1_deg5.094
r_mcangle_it1.677
r_mcbond_it1.128
r_angle_refined_deg1.012
r_scangle_it0.881
r_scbond_it0.516
r_chiral_restr0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.641
r_dihedral_angle_4_deg19.146
r_dihedral_angle_3_deg15.32
r_dihedral_angle_1_deg5.094
r_mcangle_it1.677
r_mcbond_it1.128
r_angle_refined_deg1.012
r_scangle_it0.881
r_scbond_it0.516
r_chiral_restr0.07
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13096
Nucleic Acid Atoms
Solvent Atoms1160
Heterogen Atoms480

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling