X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29120% 5000MME, 200mM ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.8757.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.051α = 90
b = 93.929β = 92.72
c = 75.215γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2014-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
12.175094.60.0640.05620.863.642667
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)
12.172.2159.70.1864.193

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 REPLACEMENTTHROUGHOUT3VYN2.175040491215395.450.183070.180360.23386RANDOM27.029
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]
0.66-0.751.39-1.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.579
r_dihedral_angle_4_deg17.548
r_dihedral_angle_3_deg16.383
r_dihedral_angle_1_deg7.274
r_long_range_B_refined5.876
r_long_range_B_other5.876
r_scangle_other4.071
r_mcangle_it2.878
r_mcangle_other2.878
r_scbond_it2.748
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.579
r_dihedral_angle_4_deg17.548
r_dihedral_angle_3_deg16.383
r_dihedral_angle_1_deg7.274
r_long_range_B_refined5.876
r_long_range_B_other5.876
r_scangle_other4.071
r_mcangle_it2.878
r_mcangle_other2.878
r_scbond_it2.748
r_scbond_other2.743
r_mcbond_it1.954
r_mcbond_other1.954
r_angle_refined_deg1.929
r_angle_other_deg1.079
r_chiral_restr0.128
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
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 Atoms5292
Nucleic Acid Atoms
Solvent Atoms462
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-3000data reduction
SCALAdata scaling