2XF4

Crystal structure of Salmonella enterica serovar typhimurium YcbL


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M MES, 1.5M SODIUM PHOSPHATE (FINAL PH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.9858.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.363α = 90
b = 124.363β = 90
c = 35.594γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
12.35096.90.146.3429.21266511

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 DIFFRACTIONOTHERTHROUGHOUTNONE2.3501194761896.80.194710.19290.22896RANDOM19.067
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]
-0.18-0.180.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.802
r_dihedral_angle_4_deg15.617
r_dihedral_angle_3_deg13.34
r_dihedral_angle_1_deg5.563
r_scangle_it2.242
r_scbond_it1.277
r_angle_refined_deg1.137
r_mcangle_it0.67
r_mcbond_it0.329
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.802
r_dihedral_angle_4_deg15.617
r_dihedral_angle_3_deg13.34
r_dihedral_angle_1_deg5.563
r_scangle_it2.242
r_scbond_it1.277
r_angle_refined_deg1.137
r_mcangle_it0.67
r_mcbond_it0.329
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.005
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_bond_other_d
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_mcangle_other
r_gen_planes_other
r_scbond_other
r_nbd_refined
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1626
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement