X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GI7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42930.1 M phosphate-citrate buffer pH 4.0 40% (v/v) PEG-300
Crystal Properties
Matthews coefficientSolvent content
2.550.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.65α = 90
b = 44.05β = 104.69
c = 117.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2013-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.99999SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9113.8195.10.0810.9952.15887325.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9493.31.080.621.12.1

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 REPLACEMENTTHROUGHOUT2GI71.9113.8155826296794.620.223090.221170.25967RANDOM33.189
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]
-0.610.06-0.480.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.025
r_dihedral_angle_4_deg16.737
r_dihedral_angle_3_deg14.435
r_dihedral_angle_1_deg7.032
r_long_range_B_refined6.225
r_long_range_B_other6.139
r_scangle_other3.605
r_mcangle_it3.314
r_mcangle_other3.314
r_scbond_it2.201
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.025
r_dihedral_angle_4_deg16.737
r_dihedral_angle_3_deg14.435
r_dihedral_angle_1_deg7.032
r_long_range_B_refined6.225
r_long_range_B_other6.139
r_scangle_other3.605
r_mcangle_it3.314
r_mcangle_other3.314
r_scbond_it2.201
r_scbond_other2.201
r_mcbond_it1.984
r_mcbond_other1.982
r_angle_refined_deg1.48
r_angle_other_deg0.779
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5426
Nucleic Acid Atoms
Solvent Atoms344
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing