1VJL | pdb_00001vjl

Crystal structure of a duf151 family protein (tm0160) from thermotoga maritima at 1.90 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP7.529310 % isopropanol, 20 % PEG 4000; 0.1 M HEPES pH7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
2VAPOR DIFFUSION,SITTING DROP,NANODROP7.527710 % isopropanol, 20 % PEG 4000; 0.1 M HEPES pH7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.509α = 90
b = 51.061β = 97.39
c = 72.974γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2003-06-15MSINGLE WAVELENGTH
21x-rayCCDADSC2003-06-15MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.3ALS5.0.3
2SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

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
1,21.9501000.08619.582.182418242.13
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)
1,21.91.9792.40.4851.441.31

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.932.9623110121496.50.2010.1980.20650.2530.255RANDOM41.4
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]
-3.30.251.362.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.589
r_dihedral_angle_4_deg23.207
r_dihedral_angle_3_deg16.655
r_dihedral_angle_1_deg6.207
r_scangle_it3.298
r_scbond_it2.259
r_angle_refined_deg1.665
r_mcangle_it1.47
r_mcbond_it1.079
r_angle_other_deg0.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.589
r_dihedral_angle_4_deg23.207
r_dihedral_angle_3_deg16.655
r_dihedral_angle_1_deg6.207
r_scangle_it3.298
r_scbond_it2.259
r_angle_refined_deg1.665
r_mcangle_it1.47
r_mcbond_it1.079
r_angle_other_deg0.813
r_symmetry_vdw_other0.219
r_nbd_refined0.204
r_nbd_other0.187
r_symmetry_vdw_refined0.115
r_chiral_restr0.103
r_symmetry_hbond_refined0.103
r_nbtor_other0.089
r_xyhbond_nbd_refined0.033
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2175
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms8

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMACrefinement
RESOLVEphasing