3TRL

Crystal structure of M-PMV dUTPASE post-inversion product (dUMP) complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D4LPDB ENTRY 2D4L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.827α = 90
b = 60.827β = 90
c = 63.999γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2004-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8128EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.82098.20.06312.23.21231212312-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.91000.4633.13.11861

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONrigid body refinementTHROUGHOUTPDB ENTRY 2D4L1.820123101165765398.190.162550.16110.18794RANDOM33.508
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]
1.280.641.28-1.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.438
r_dihedral_angle_4_deg32.157
r_dihedral_angle_3_deg15.015
r_dihedral_angle_1_deg5.928
r_scangle_it4.429
r_scbond_it2.632
r_mcangle_it2.516
r_angle_refined_deg1.825
r_mcbond_it1.66
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.438
r_dihedral_angle_4_deg32.157
r_dihedral_angle_3_deg15.015
r_dihedral_angle_1_deg5.928
r_scangle_it4.429
r_scbond_it2.632
r_mcangle_it2.516
r_angle_refined_deg1.825
r_mcbond_it1.66
r_nbtor_refined0.316
r_symmetry_hbond_refined0.229
r_nbd_refined0.216
r_xyhbond_nbd_refined0.215
r_symmetry_vdw_refined0.158
r_chiral_restr0.124
r_bond_refined_d0.02
r_gen_planes_refined0.008
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 Atoms821
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms20

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing