7P1E

Structure of KDNase from Aspergillus Terrerus in complex with 2,3-difluoro-2-keto-3-deoxynononic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629320% PEG 6K, 0.1M MES pH6 , 0.2M Calcium Chloride
Crystal Properties
Matthews coefficientSolvent content
2.1442.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.348α = 90
b = 66.743β = 90
c = 92.635γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173PIXELDECTRIS PILATUS 6M-F2018-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.5361.3599.80.1090.9957.32.658094
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.5799.91.2720.5312.6

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 REPLACEMENTTHROUGHOUT2xcy1.5361.3555146289399.220.18730.18570.2202RANDOM19.55
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]
-10.060.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.913
r_dihedral_angle_4_deg14.551
r_dihedral_angle_3_deg11.201
r_dihedral_angle_1_deg6.687
r_angle_refined_deg1.434
r_angle_other_deg0.745
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.913
r_dihedral_angle_4_deg14.551
r_dihedral_angle_3_deg11.201
r_dihedral_angle_1_deg6.687
r_angle_refined_deg1.434
r_angle_other_deg0.745
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2941
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing