2D4L

Crystal structure of truncated in C-terminal M-PMV dUTPase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 8000, AMMONIUM CHLORIDE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.1442.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.163α = 90
b = 61.163β = 90
c = 64.167γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2005-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.843EMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.75398.340.0370.03121.153.081481314813-333.811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.8980.5330.443.333.092308

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2AKV1.720140131401380098.340.16320.16320.16230.17888RANDOM31.803
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]
1.220.611.22-1.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.506
r_scangle_it15.06
r_dihedral_angle_3_deg13.575
r_scbond_it12.776
r_dihedral_angle_1_deg12.202
r_dihedral_angle_4_deg9.046
r_mcangle_it5.274
r_mcbond_it2.338
r_angle_refined_deg1.948
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.506
r_scangle_it15.06
r_dihedral_angle_3_deg13.575
r_scbond_it12.776
r_dihedral_angle_1_deg12.202
r_dihedral_angle_4_deg9.046
r_mcangle_it5.274
r_mcbond_it2.338
r_angle_refined_deg1.948
r_nbtor_refined0.32
r_nbd_refined0.225
r_xyhbond_nbd_refined0.195
r_symmetry_vdw_refined0.193
r_symmetry_hbond_refined0.144
r_chiral_restr0.141
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms828
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling