5A1J

Periplasmic Binding Protein CeuE in complex with ferric 4-LICAM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CHUPDB ENTRY 2CHU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.2M SODIUM NITRATE, 0.1M BIS TRIS PROPANE PH 7.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.243

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.42α = 90
b = 66.89β = 90
c = 67.3γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I24DiamondI24

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
11.6144.9699.50.0518.35.72042892
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)
11.611.6594.90.422.23

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2CHU1.633.6534006177397.750.26660.264220.31242RANDOM20.566
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]
-7.831.396.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.219
r_dihedral_angle_3_deg19.736
r_dihedral_angle_4_deg8.236
r_dihedral_angle_1_deg7.343
r_angle_refined_deg2.37
r_mcangle_it2.157
r_mcbond_it1.549
r_mcbond_other1.549
r_scbond_it1.459
r_angle_other_deg1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.219
r_dihedral_angle_3_deg19.736
r_dihedral_angle_4_deg8.236
r_dihedral_angle_1_deg7.343
r_angle_refined_deg2.37
r_mcangle_it2.157
r_mcbond_it1.549
r_mcbond_other1.549
r_scbond_it1.459
r_angle_other_deg1.07
r_chiral_restr0.132
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2243
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
MOLREPphasing