X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KG6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.52931.3 M tri-sodium citrate, 30 mM (D)+sucrose, 100 mM tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.122α = 90
b = 94.301β = 90
c = 150.989γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMIRRORS2009-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.750980.0720.07220.16.85947724
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)
11.71.7685.80.6562.35.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KG71.730.7759373593733003980.1840.1820.217RANDOM26.94
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]
0.41-0.650.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.688
r_dihedral_angle_3_deg13.081
r_dihedral_angle_4_deg9.132
r_dihedral_angle_1_deg5.463
r_scangle_it2.846
r_mcangle_it2.449
r_scbond_it1.867
r_mcbond_it1.661
r_angle_refined_deg1.121
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.688
r_dihedral_angle_3_deg13.081
r_dihedral_angle_4_deg9.132
r_dihedral_angle_1_deg5.463
r_scangle_it2.846
r_mcangle_it2.449
r_scbond_it1.867
r_mcbond_it1.661
r_angle_refined_deg1.121
r_nbtor_refined0.302
r_nbd_refined0.195
r_symmetry_vdw_refined0.187
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.129
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms4381
Nucleic Acid Atoms
Solvent Atoms502
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling