7P1F

Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% PEG 6K, 0.1M MES pH6 , 0.2M Calcium Chloride
Crystal Properties
Matthews coefficientSolvent content
2.2745.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.318α = 90
b = 66.833β = 90.76
c = 92.813γ = 90
Symmetry
Space GroupP 1 2 1

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
11.2992.896.30.0590.9967.62.6129965
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)
11.291.3186.60.680.479

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 REPLACEMENTTHROUGHOUT2xzk1.4592.8123439648197.830.15440.15210.1986RANDOM17.116
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]
0.22-0.57-1.080.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.14
r_sphericity_free28.679
r_sphericity_bonded14.726
r_dihedral_angle_4_deg13.495
r_dihedral_angle_3_deg11.301
r_dihedral_angle_1_deg6.807
r_rigid_bond_restr4.943
r_angle_refined_deg1.411
r_angle_other_deg0.735
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.14
r_sphericity_free28.679
r_sphericity_bonded14.726
r_dihedral_angle_4_deg13.495
r_dihedral_angle_3_deg11.301
r_dihedral_angle_1_deg6.807
r_rigid_bond_restr4.943
r_angle_refined_deg1.411
r_angle_other_deg0.735
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5906
Nucleic Acid Atoms
Solvent Atoms874
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing