7P1Q

Structure of KDNase from Trichophyton Rubrum in complex with 2-keto-3-deoxynononic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829325% PEG 1500, 0.1M MMT pH8
Crystal Properties
Matthews coefficientSolvent content
2.2545.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.922α = 90
b = 74.472β = 90
c = 161.365γ = 90
Symmetry
Space GroupC 2 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)Rrim I (All)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
10.9180.6984.30.0480.99914.65.2226869
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.910.930.8210.534

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 REPLACEMENTTHROUGHOUT2xzj0.9180.682155701121984.320.14110.14030.1556RANDOM11
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]
-1.090.780.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.742
r_sphericity_free23.07
r_dihedral_angle_4_deg15.303
r_sphericity_bonded11.401
r_dihedral_angle_3_deg10.754
r_dihedral_angle_1_deg7.217
r_rigid_bond_restr4.817
r_angle_refined_deg1.565
r_angle_other_deg0.878
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.742
r_sphericity_free23.07
r_dihedral_angle_4_deg15.303
r_sphericity_bonded11.401
r_dihedral_angle_3_deg10.754
r_dihedral_angle_1_deg7.217
r_rigid_bond_restr4.817
r_angle_refined_deg1.565
r_angle_other_deg0.878
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2938
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing