5OPK

Crystal structure of D52N/R367Q cN-II mutant bound to dATP and free phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5K7Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M MES/imidazole pH 6.5; 0.03 M of each divalent cation; 10% w/v PEG 8000, 20% v/v ethylene glycol (Morpheus condition A2)
Crystal Properties
Matthews coefficientSolvent content
3.4364.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.579α = 90
b = 127.104β = 90
c = 130.317γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.73648.9998.80.0930.1010.99813.66.57760729.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.8494.60.830.9050.8231.886.21

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 REPLACEMENTTHROUGHOUT5K7Y1.7448.9973724388198.80.17970.17850.2034RANDOM29.152
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.927
r_dihedral_angle_4_deg16.702
r_dihedral_angle_3_deg13.14
r_dihedral_angle_1_deg6.133
r_angle_other_deg3.598
r_angle_refined_deg1.569
r_chiral_restr0.096
r_gen_planes_other0.015
r_bond_refined_d0.013
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.927
r_dihedral_angle_4_deg16.702
r_dihedral_angle_3_deg13.14
r_dihedral_angle_1_deg6.133
r_angle_other_deg3.598
r_angle_refined_deg1.569
r_chiral_restr0.096
r_gen_planes_other0.015
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3843
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
XDSdata processing
XSCALEdata reduction
Cootmodel building