4YVU

Crystal structure of CotA native enzyme in the acid condition, PH5.6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GSK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629330-42%(v/v) ethylene glycol,100mM sodium citrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
3.4664.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.73α = 90
b = 101.73β = 90
c = 135.572γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2013-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBSRF BEAMLINE 3W1A1.0000BSRF3W1A

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
12.329.41000.09712.23.736605
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)
12.32.341000.2814.63.7

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 REPLACEMENTTHROUGHOUT1GSK2.329.3834656182499.640.160410.158990.18693RANDOM21.344
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]
0.10.10.1-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.698
r_dihedral_angle_4_deg20.371
r_dihedral_angle_3_deg13.506
r_dihedral_angle_1_deg7.282
r_long_range_B_refined5.895
r_long_range_B_other5.492
r_scangle_other3.364
r_mcangle_other2.545
r_mcangle_it2.542
r_scbond_it2.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.698
r_dihedral_angle_4_deg20.371
r_dihedral_angle_3_deg13.506
r_dihedral_angle_1_deg7.282
r_long_range_B_refined5.895
r_long_range_B_other5.492
r_scangle_other3.364
r_mcangle_other2.545
r_mcangle_it2.542
r_scbond_it2.067
r_scbond_other2.067
r_angle_refined_deg1.594
r_mcbond_it1.565
r_mcbond_other1.557
r_angle_other_deg0.791
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4080
Nucleic Acid Atoms
Solvent Atoms405
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing