2CIC

THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE WITH SUBSTRATE ANALOGUE DUPNHPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W2YPDB ENTRY 1W2Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13.5 M SODIUM FORMATE PH 7.0, 20 MM MAGNESIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.397α = 90
b = 93.397β = 90
c = 143.634γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002004-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.73097.80.0537.18.1330923
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)
11.71.7690.80.33.34.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1W2Y1.73031466170094.20.1620.1590.206RANDOM20.21
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]
0.540.54-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.784
r_dihedral_angle_4_deg16.907
r_dihedral_angle_3_deg13.984
r_dihedral_angle_1_deg5.544
r_scangle_it3.786
r_scbond_it2.74
r_angle_other_deg1.967
r_angle_refined_deg1.928
r_mcangle_it1.842
r_mcbond_it1.483
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.784
r_dihedral_angle_4_deg16.907
r_dihedral_angle_3_deg13.984
r_dihedral_angle_1_deg5.544
r_scangle_it3.786
r_scbond_it2.74
r_angle_other_deg1.967
r_angle_refined_deg1.928
r_mcangle_it1.842
r_mcbond_it1.483
r_symmetry_hbond_refined0.392
r_nbd_refined0.349
r_xyhbond_nbd_refined0.331
r_symmetry_vdw_other0.285
r_symmetry_vdw_refined0.281
r_nbd_other0.26
r_chiral_restr0.199
r_nbtor_refined0.196
r_nbtor_other0.095
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1851
Nucleic Acid Atoms
Solvent Atoms478
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing