3TE8

Crystal structure of risS periplasmic domain at low pH dimer with N-termini ordered


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5289BupsA.00863.i.A1 PW25353 at 2327 mg/mL against 10% PEG 1000, 10% PEG 8000, crystal tracking ID 221872c12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.8433.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.06α = 90
b = 56.02β = 96.03
c = 46.81γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002011-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

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
11.75098.10.04919.094.82333822891-329.204
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)
11.71.7497.40.4564.53

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 REPLACEMENTTHROUGHOUT3LR01.746.5522860116997.960.18390.18150.2281RANDOM26.0146
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]
-0.28-0.01-0.420.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.189
r_dihedral_angle_4_deg18.389
r_dihedral_angle_3_deg11.545
r_dihedral_angle_1_deg6.013
r_angle_refined_deg1.597
r_angle_other_deg1.309
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.189
r_dihedral_angle_4_deg18.389
r_dihedral_angle_3_deg11.545
r_dihedral_angle_1_deg6.013
r_angle_refined_deg1.597
r_angle_other_deg1.309
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1911
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction