1YE8

Crystal Structure of THEP1 from the hyperthermophile Aquifex aeolicus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.7293PEG 3350, potassium dihydrogenphosphate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.87α = 90
b = 64.24β = 105.23
c = 39.62γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMirrors2003-12-21MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.97625, 0.979802SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.418.2195.30.0840.05711.673.5331813318120.86
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.590.60.3970.3733.493.411436

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.418.213241931502167997.170.173510.173510.171680.20749RANDOM17.304
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]
-0.83-0.560.71-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.296
r_scangle_it3.629
r_sphericity_free2.393
r_scbond_it2.294
r_sphericity_bonded2.284
r_mcangle_it1.606
r_angle_refined_deg1.334
r_rigid_bond_restr1.1
r_mcbond_it0.961
r_metal_ion_refined0.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.296
r_scangle_it3.629
r_sphericity_free2.393
r_scbond_it2.294
r_sphericity_bonded2.284
r_mcangle_it1.606
r_angle_refined_deg1.334
r_rigid_bond_restr1.1
r_mcbond_it0.961
r_metal_ion_refined0.518
r_nbd_refined0.198
r_symmetry_vdw_refined0.157
r_symmetry_hbond_refined0.114
r_xyhbond_nbd_refined0.111
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1399
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms8

Software

Software
Software NamePurpose
XDSdata scaling
XDSdata reduction
SHARPphasing
REFMACrefinement