4EQV

Structure of Saccharomyces cerevisiae invertase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52933% PEG 3350, 5% MPD, 0.6M Magnesium formate, 1mM TCEP, 75 mM Guanidinium chloride, 0.1 Bis-Tris pH 6.5 (2:1), VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.9975.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 268.659α = 90
b = 268.659β = 90
c = 224.452γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 315r2011-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
13.356.3198.50.0970.0978.16.4137870166.21
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)
13.33.4892.60.7980.37725

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KF33.456.311137870636198.80.2220.2210.239RANDOM51.16
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]
-0.25-0.250.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.274
r_dihedral_angle_3_deg19.031
r_dihedral_angle_4_deg14.478
r_dihedral_angle_1_deg6.522
r_angle_refined_deg1.176
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.274
r_dihedral_angle_3_deg19.031
r_dihedral_angle_4_deg14.478
r_dihedral_angle_1_deg6.522
r_angle_refined_deg1.176
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.006
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms32992
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling