X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WNB2WNB and 4JS2
experimental modelPDB 4JS22WNB and 4JS2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529318-21% PEG3350, 30 mM sodium tartrate, 100 mM sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.2762.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.17α = 90
b = 94.22β = 90
c = 126.19γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002013-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.752.4397.40.1410.0810.9865.53.328543
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8399.10.9010.5420.4221.43.33789

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2WNB and 4JS22.752.4327051145096.530.19580.19310.2461RANDOM59.972
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]
-1.263.72-2.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg21.195
r_dihedral_angle_3_deg16.457
r_mcangle_it6.566
r_dihedral_angle_1_deg6.243
r_mcbond_it4.382
r_mcbond_other4.363
r_angle_refined_deg1.799
r_angle_other_deg1.304
r_chiral_restr0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.088
r_dihedral_angle_4_deg21.195
r_dihedral_angle_3_deg16.457
r_mcangle_it6.566
r_dihedral_angle_1_deg6.243
r_mcbond_it4.382
r_mcbond_other4.363
r_angle_refined_deg1.799
r_angle_other_deg1.304
r_chiral_restr0.132
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4548
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms266

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing