3P24

Structure of profragilysin-3 from Bacteroides fragilis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5297100mM sodium citrate dihydrate, 20% PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.5651.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.74α = 90
b = 69.14β = 91.57
c = 158.91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.0723ESRFID23-1

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
11.85098.90.075164503164503

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.85016450316372278198.890.169880.169710.20436RANDOM33.719
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]
-0.30.050.4-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.952
r_dihedral_angle_3_deg13.341
r_dihedral_angle_4_deg12.933
r_dihedral_angle_1_deg6.396
r_scangle_it3.331
r_scbond_it2.072
r_mcangle_it1.463
r_angle_refined_deg1.271
r_angle_other_deg0.824
r_mcbond_it0.792
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.952
r_dihedral_angle_3_deg13.341
r_dihedral_angle_4_deg12.933
r_dihedral_angle_1_deg6.396
r_scangle_it3.331
r_scbond_it2.072
r_mcangle_it1.463
r_angle_refined_deg1.271
r_angle_other_deg0.824
r_mcbond_it0.792
r_mcbond_other0.181
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11311
Nucleic Acid Atoms
Solvent Atoms1147
Heterogen Atoms75

Software

Software
Software NamePurpose
ProDCdata collection
SHELXSphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling