2XOL

High resolution structure of TtrD from Archaeoglobus fulgidus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IDGPDB ENTRY 2IDG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.2 M SODIUM FORMATE, 20% PEG 3350, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6353.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.763α = 90
b = 52.537β = 91.26
c = 64.947γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.3564.6996.90.0517.66.98970014.78
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)
11.351.4294.90.494.26.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2IDG1.3564.9385158452396.60.152480.151160.17751RANDOM16.751
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]
0.030.170.2-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.876
r_dihedral_angle_4_deg21.578
r_dihedral_angle_3_deg13.372
r_scangle_it7.335
r_scbond_it5.082
r_dihedral_angle_1_deg4.518
r_mcangle_it3.598
r_mcbond_it2.4
r_rigid_bond_restr1.34
r_angle_refined_deg1.277
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.876
r_dihedral_angle_4_deg21.578
r_dihedral_angle_3_deg13.372
r_scangle_it7.335
r_scbond_it5.082
r_dihedral_angle_1_deg4.518
r_mcangle_it3.598
r_mcbond_it2.4
r_rigid_bond_restr1.34
r_angle_refined_deg1.277
r_mcbond_other0.953
r_angle_other_deg0.895
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2782
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing