4YVN

Crystal structure of CotA laccase complexed with ABTS at a novel binding site


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
3.4864.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.993α = 90
b = 101.993β = 90
c = 135.791γ = 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
12.329.499.90.1479.64.336864
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)
12.32.341000.2556.54.4

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 REPLACEMENTTHROUGHOUT1GSK2.329.434956183799.770.159650.157830.19441RANDOM22.07
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]
0.150.150.15-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.66
r_dihedral_angle_4_deg21.969
r_dihedral_angle_3_deg13.795
r_dihedral_angle_1_deg7.057
r_long_range_B_refined6.343
r_long_range_B_other6.12
r_scangle_other3.818
r_mcangle_it3.121
r_mcangle_other3.12
r_scbond_it2.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.66
r_dihedral_angle_4_deg21.969
r_dihedral_angle_3_deg13.795
r_dihedral_angle_1_deg7.057
r_long_range_B_refined6.343
r_long_range_B_other6.12
r_scangle_other3.818
r_mcangle_it3.121
r_mcangle_other3.12
r_scbond_it2.316
r_scbond_other2.316
r_mcbond_it1.914
r_mcbond_other1.907
r_angle_refined_deg1.647
r_angle_other_deg0.794
r_chiral_restr0.096
r_bond_refined_d0.015
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 Atoms4070
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms61

Software

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