X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.53000.1 M sodium cacadylate, pH 5.5, 0.14 M Ca(Ac)2, 13 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.6954.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.609α = 90
b = 148.416β = 98.88
c = 64.029γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-05-18MSINGLE 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
11.738.4197.30.04915.13.4115043115043
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)
11.71.7998.30.6510.6511.23.516950

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 REPLACEMENTTHROUGHOUT4DUD1.738.41114028114028570796.40.170.170.16780.2113RANDOM21.8807
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]
-1.050.361.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.505
r_dihedral_angle_4_deg18.411
r_dihedral_angle_3_deg14.411
r_dihedral_angle_1_deg6.539
r_scangle_it5.608
r_scbond_it3.641
r_mcangle_it2.298
r_angle_refined_deg2.159
r_mcbond_it1.419
r_chiral_restr0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.505
r_dihedral_angle_4_deg18.411
r_dihedral_angle_3_deg14.411
r_dihedral_angle_1_deg6.539
r_scangle_it5.608
r_scbond_it3.641
r_mcangle_it2.298
r_angle_refined_deg2.159
r_mcbond_it1.419
r_chiral_restr0.17
r_bond_refined_d0.027
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7232
Nucleic Acid Atoms
Solvent Atoms830
Heterogen Atoms112

Software

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