1SJ5

Crystal structure of a duf151 family protein (tm0160) from thermotoga maritima at 2.8 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.9pH 6.90
Crystal Properties
Matthew coefficientSolvent content
2.2645.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.001α = 90
b = 52.136β = 97.64
c = 73.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90IMAGE PLATERIGAKU RAXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
12.872.5598.20.079128172
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)
12.82.998.90.6523.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1O5Y2.872.55776234998.20.218580.215710.27555RANDOM22.388
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]
-3.52-1.261.551.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.853
r_scangle_it4.847
r_scbond_it3.309
r_angle_refined_deg1.635
r_mcangle_it1.061
r_angle_other_deg0.878
r_mcbond_it0.441
r_symmetry_hbond_refined0.323
r_symmetry_vdw_other0.28
r_nbd_refined0.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.853
r_scangle_it4.847
r_scbond_it3.309
r_angle_refined_deg1.635
r_mcangle_it1.061
r_angle_other_deg0.878
r_mcbond_it0.441
r_symmetry_hbond_refined0.323
r_symmetry_vdw_other0.28
r_nbd_refined0.232
r_nbd_other0.231
r_symmetry_vdw_refined0.211
r_xyhbond_nbd_refined0.159
r_nbtor_other0.088
r_chiral_restr0.081
r_bond_refined_d0.017
r_gen_planes_other0.007
r_gen_planes_refined0.006
r_bond_other_d0.003
r_xyhbond_nbd_other
r_nbtor_refined
r_metal_ion_other
r_symmetry_hbond_other
r_metal_ion_refined
r_mcbond_other
r_dihedral_angle_4_deg
r_dihedral_angle_3_deg
r_dihedral_angle_2_deg
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2173
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
HKL-2000data reduction
CCP4phasing