3VTH

Crystal structure of full-length HypF in the phosphate- and nucleotide-bound form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82880.1M imidazole, 1.8M Na/K phosphate, 0.2M NaCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.9658.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 232.983α = 90
b = 232.983β = 90
c = 65.665γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2011-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9000SPring-8BL44XU

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
1220980.09618.46.313517613517631.4
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)
122.0396.80.4974.25.26623

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2201268356631970.210760.209350.23758RANDOM46.815
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]
-0.95-0.47-0.951.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.966
r_dihedral_angle_3_deg14.925
r_dihedral_angle_4_deg14.536
r_dihedral_angle_1_deg5.685
r_scangle_it2.918
r_scbond_it1.747
r_angle_refined_deg1.255
r_mcangle_it1.021
r_mcbond_it0.524
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.966
r_dihedral_angle_3_deg14.925
r_dihedral_angle_4_deg14.536
r_dihedral_angle_1_deg5.685
r_scangle_it2.918
r_scbond_it1.747
r_angle_refined_deg1.255
r_mcangle_it1.021
r_mcbond_it0.524
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11094
Nucleic Acid Atoms
Solvent Atoms507
Heterogen Atoms176

Software

Software
Software NamePurpose
BSSdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling