6VLO

X-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoeba polyphaga Minivirus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529313-16% PEG-5000, 2% ethylene glycol, 100 mM HEPES, in the presence of 5 mM dTDP
Crystal Properties
Matthews coefficientSolvent content
2.3447.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.883α = 90
b = 111.083β = 90
c = 133.385γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2018-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97918APS19-BM

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
12.055099.50.08644.58.387647
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)
12.052.0998.40.2985.8

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 REPLACEMENTTHROUGHOUT1R662.0538.8883130451799.240.1830.18050.2291RANDOM33.577
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]
0.060.6-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.6
r_dihedral_angle_3_deg16.013
r_dihedral_angle_4_deg13.021
r_dihedral_angle_1_deg7.101
r_angle_refined_deg1.559
r_angle_other_deg1.337
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.6
r_dihedral_angle_3_deg16.013
r_dihedral_angle_4_deg13.021
r_dihedral_angle_1_deg7.101
r_angle_refined_deg1.559
r_angle_other_deg1.337
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10133
Nucleic Acid Atoms
Solvent Atoms488
Heterogen Atoms245

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing