X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UKV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.929314% PEG MME 2000, 100 mM Tris-Acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.66α = 90
b = 120.23β = 90.67
c = 60.55γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.934ESRFID14-2

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
11.4819.9296.50.07611.32113100109178-3-324
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.481.4975.1

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1ukv1.4819.92109178103719545996.50.164860.164860.163360.19283RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.495
r_dihedral_angle_4_deg18.665
r_dihedral_angle_3_deg13.621
r_dihedral_angle_1_deg5.76
r_sphericity_free5.636
r_sphericity_bonded3.804
r_scangle_it3.696
r_scbond_it2.919
r_rigid_bond_restr2.137
r_mcangle_it2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.495
r_dihedral_angle_4_deg18.665
r_dihedral_angle_3_deg13.621
r_dihedral_angle_1_deg5.76
r_sphericity_free5.636
r_sphericity_bonded3.804
r_scangle_it3.696
r_scbond_it2.919
r_rigid_bond_restr2.137
r_mcangle_it2
r_angle_refined_deg1.453
r_mcbond_it1.345
r_nbtor_refined0.307
r_nbd_refined0.206
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.148
r_symmetry_hbond_refined0.123
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5268
Nucleic Acid Atoms
Solvent Atoms923
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
ProDCdata collection
XDSdata scaling