X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E6IPDB entry 3E6I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M Na HEPES pH 7.5, 5% Isopropanol, 22% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5952.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.185α = 90
b = 71.185β = 90
c = 224.862γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDmirrors2009-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.979SSRLBL9-2

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
12.938.0198.30.1234.224282
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.92.9899.10.4362.54.3

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 REPLACEMENTTHROUGHOUTPDB entry 3E6I2.935.5923000121798.080.21070.206470.29199RANDOM50.771
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]
0.060.06-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.649
r_dihedral_angle_4_deg22.328
r_dihedral_angle_3_deg20.989
r_dihedral_angle_1_deg6.626
r_scangle_it2.586
r_angle_refined_deg1.527
r_scbond_it1.472
r_mcangle_it1.083
r_mcbond_it0.553
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.649
r_dihedral_angle_4_deg22.328
r_dihedral_angle_3_deg20.989
r_dihedral_angle_1_deg6.626
r_scangle_it2.586
r_angle_refined_deg1.527
r_scbond_it1.472
r_mcangle_it1.083
r_mcbond_it0.553
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms7554
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms116

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling