X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FNAPDB ENTRIES 1FNA AND 2EKE
experimental modelPDB 2EKEPDB ENTRIES 1FNA AND 2EKE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829214% PEG8000, 16% glycerol, pH 8.0, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.261.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.637α = 90
b = 175.462β = 90
c = 52.83γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-ID-F

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
12.4501000.08518.97.12258622586
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)
12.3952.45796.290.6432.156.6

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1FNA AND 2EKE2.4202134121341115199.740.225580.225580.22310.27158RANDOM49.816
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]
-0.67-0.030.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.575
r_dihedral_angle_3_deg19.323
r_dihedral_angle_4_deg18.328
r_dihedral_angle_1_deg7.806
r_scangle_it3.918
r_scbond_it2.568
r_mcangle_it1.923
r_angle_refined_deg1.864
r_mcbond_it1.107
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.575
r_dihedral_angle_3_deg19.323
r_dihedral_angle_4_deg18.328
r_dihedral_angle_1_deg7.806
r_scangle_it3.918
r_scbond_it2.568
r_mcangle_it1.923
r_angle_refined_deg1.864
r_mcbond_it1.107
r_nbtor_refined0.308
r_symmetry_vdw_refined0.27
r_nbd_refined0.232
r_chiral_restr0.16
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.14
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2666
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms48

Software

Software
Software NamePurpose
MD2data collection
MAR345data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling