3A7N

Crystal structure of uracil-DNA glycosylase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZHXPDB ENTRY 2ZHX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH72981.8M tri-ammonium citrate pH 7.0, 10% isopropanol, microbatch, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3948.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.84α = 90
b = 63.67β = 90
c = 86.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2008-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
11.953098.20.113.74.81862818238130
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)
1.952.0697.70.4933.24.62583

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ZHX1.9526.24186281731988597.740.181950.181030.19888RANDOM19.059
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]
-0.560.090.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.631
r_dihedral_angle_4_deg18.539
r_dihedral_angle_3_deg12.806
r_dihedral_angle_1_deg5.05
r_scangle_it1.55
r_angle_refined_deg1.139
r_scbond_it0.919
r_mcangle_it0.591
r_mcbond_it0.337
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.631
r_dihedral_angle_4_deg18.539
r_dihedral_angle_3_deg12.806
r_dihedral_angle_1_deg5.05
r_scangle_it1.55
r_angle_refined_deg1.139
r_scbond_it0.919
r_mcangle_it0.591
r_mcbond_it0.337
r_nbtor_refined0.301
r_nbd_refined0.191
r_symmetry_vdw_refined0.167
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.115
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms1764
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms26

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling