X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429330% PEG4000, 0.3M Lithium Sulfate, 0.1 M Sodium Acetate and 0.1 M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.4850.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.62α = 109.38
b = 68.48β = 92.66
c = 87.07γ = 117.66
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9801SOLEILPROXIMA 1

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
12.2549.3897.90.121113.9755653
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)
12.252.3395.690.570.4832.46

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 REPLACEMENTTHROUGHOUT2IVP2.3349.3852870278397.920.204790.202290.25265RANDOM35.999
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]
-0.22-0.15-0.050.080.53-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.596
r_dihedral_angle_4_deg18.838
r_dihedral_angle_3_deg12.955
r_dihedral_angle_1_deg6.016
r_long_range_B_refined5.215
r_long_range_B_other5.167
r_scangle_other4.031
r_mcangle_it2.784
r_mcangle_other2.784
r_scbond_it2.727
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.596
r_dihedral_angle_4_deg18.838
r_dihedral_angle_3_deg12.955
r_dihedral_angle_1_deg6.016
r_long_range_B_refined5.215
r_long_range_B_other5.167
r_scangle_other4.031
r_mcangle_it2.784
r_mcangle_other2.784
r_scbond_it2.727
r_scbond_other2.727
r_mcbond_it1.918
r_mcbond_other1.901
r_angle_refined_deg1.662
r_angle_other_deg0.777
r_chiral_restr0.085
r_bond_refined_d0.014
r_gen_planes_refined0.013
r_gen_planes_other0.009
r_bond_other_d0.008
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 Atoms8410
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms164

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
MOLREPphasing