2VLI | pdb_00002vli

Structure of Deinococcus radiodurans tunicamycin resistance protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529320 DEGREESC AFTER 3-6 DAYS USING HANGING DROPS CONTAINING 2 MICROL OF THE PROTEIN, 0.4-0.8 MICROL 0.1 M CDCL2 AND 1.6-1.2 MICROL OF A RESERVOIR SOLUTION CONTAINING 11-13% PEG 4000, 0.8 M SODIUM FORMATE AND 0.1 M SODIUM ACETATE PH 5.0
Crystal Properties
Matthews coefficientSolvent content
2.1648.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.36α = 90
b = 118.16β = 90
c = 81.11γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHRH COATED TOROIDAL MIRROR2006-12-15MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9144, 0.9792ESRFID23-1

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
11.9522.9399.50.0914.544.9428689-3.719.9
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)
11.951.971000.5235.09

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTNONE1.9522.927186148699.40.1760.1740.18010.2140.2176RANDOM20.9
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]
0.39-2.532.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.162
r_dihedral_angle_4_deg18.081
r_dihedral_angle_3_deg14.279
r_dihedral_angle_1_deg5.319
r_scangle_it4.821
r_scbond_it3.206
r_mcbond_it1.959
r_mcangle_it1.933
r_angle_refined_deg1.58
r_angle_other_deg0.984
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.162
r_dihedral_angle_4_deg18.081
r_dihedral_angle_3_deg14.279
r_dihedral_angle_1_deg5.319
r_scangle_it4.821
r_scbond_it3.206
r_mcbond_it1.959
r_mcangle_it1.933
r_angle_refined_deg1.58
r_angle_other_deg0.984
r_symmetry_vdw_other0.287
r_nbd_refined0.216
r_symmetry_vdw_refined0.21
r_nbd_other0.207
r_symmetry_hbond_refined0.195
r_xyhbond_nbd_refined0.181
r_nbtor_refined0.173
r_chiral_restr0.1
r_nbtor_other0.088
r_bond_refined_d0.018
r_bond_other_d0.006
r_gen_planes_refined0.006
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 Atoms2620
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing