X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DUB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.53000.1 M sodium cacadylate, pH 5.5, 0.14 M Ca(Ac)2, 14 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.754.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.831α = 90
b = 152.297β = 94.58
c = 61.785γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-21.033SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1239.17397.50.08610.13.47111271112
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1197.70.6070.6071.23.510432

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 REPLACEMENTTHROUGHOUT4DUB238.387089670896358597.190.16250.16250.15990.212RANDOM33.183
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]
-0.680.38-0.671.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_4_deg15.783
r_dihedral_angle_3_deg14.739
r_dihedral_angle_1_deg6.644
r_scangle_it5.306
r_scbond_it3.404
r_mcangle_it1.994
r_angle_refined_deg1.896
r_mcbond_it1.157
r_chiral_restr0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_4_deg15.783
r_dihedral_angle_3_deg14.739
r_dihedral_angle_1_deg6.644
r_scangle_it5.306
r_scbond_it3.404
r_mcangle_it1.994
r_angle_refined_deg1.896
r_mcbond_it1.157
r_chiral_restr0.13
r_bond_refined_d0.023
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7261
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms96

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XSCALEdata scaling
MOLREPphasing