4D5R

Structure of N-terminally truncated A49 from Vaccinia Virus Western Reserve


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1293CRYSTALS WERE GROWN BY MIXING 2 UL PROTEIN (20-21 MG/ML) WITH 2 UL RESERVOIR SOLUTION AND EQUILIBRATING AT 20 C AGAINST 500 UL RESERVOIRS CONTAINING 1.3- 1.5 M SODIUM MALONATE PH 6.8, 1% (VOL/VOL) PEG 400 AND 4-10% (VOL/VOL) GLYCEROL, THE BEST CRYSTALS BEING OBTAINED WHEN THE RESERVOIR WAS OVERLAID WITH 100 UL OF A 1:1 MIXTURE OF PARAFFIN AND SILICONE OIL (MOLECULAR DIMENSIONS). CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION IN 2.1 M SODIUM MALONATE, 1% (VOL/VOL) PEG 400 AND 5% (VOL/VOL) GLYCEROL.
Crystal Properties
Matthews coefficientSolvent content
2.1643.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.85α = 90
b = 42.74β = 100.51
c = 67.19γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MTOROIDAL MIRRORS2013-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.93399.60.0432.214.125211-338.3
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)
11.91.95991.152.913.5

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 DIFFRACTIONSIRASTHROUGHOUTNONE1.933.0323928127999.510.187350.185210.2264RANDOM61.597
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]
-1.85-0.35.38-3.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.967
r_dihedral_angle_4_deg21.013
r_dihedral_angle_3_deg13.086
r_dihedral_angle_1_deg5.672
r_mcangle_it4.527
r_scbond_it4.518
r_mcbond_it3.548
r_mcbond_other3.545
r_angle_refined_deg1.749
r_angle_other_deg1.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.967
r_dihedral_angle_4_deg21.013
r_dihedral_angle_3_deg13.086
r_dihedral_angle_1_deg5.672
r_mcangle_it4.527
r_scbond_it4.518
r_mcbond_it3.548
r_mcbond_other3.545
r_angle_refined_deg1.749
r_angle_other_deg1.239
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.005
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2399
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing