4AKQ

Mutations in the neighbourhood of CotA-laccase trinuclear site: E498D mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W6LPDB ENTRY 1W6L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.510% PEG 4K, 0.1 M SODIUM CITRATE PH 5.5, 26% ISOPROPANOL
Crystal Properties
Matthews coefficientSolvent content
3.5465.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.833α = 90
b = 101.833β = 90
c = 136.565γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.154.0799.90.084483622
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)
12.12.211000.374

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 1W6L2.140.8245872244299.940.178760.177320.20623RANDOM27.252
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.385
r_dihedral_angle_4_deg17.565
r_dihedral_angle_3_deg13.009
r_dihedral_angle_1_deg6.118
r_scangle_it1.594
r_angle_refined_deg1.036
r_scbond_it0.969
r_mcangle_it0.769
r_mcbond_it0.445
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.385
r_dihedral_angle_4_deg17.565
r_dihedral_angle_3_deg13.009
r_dihedral_angle_1_deg6.118
r_scangle_it1.594
r_angle_refined_deg1.036
r_scbond_it0.969
r_mcangle_it0.769
r_mcbond_it0.445
r_nbtor_refined0.305
r_nbd_refined0.176
r_symmetry_vdw_refined0.126
r_symmetry_hbond_refined0.116
r_xyhbond_nbd_refined0.098
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms4069
Nucleic Acid Atoms
Solvent Atoms458
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing