2HRG

Crystal Structure of Blue Laccase from Trametes trogii complexed with p-methylbenzoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QT6Blue Laccase from Panus tigrinus (not yet deposited)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5296PEG 8000, calcium acetate, PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
3.6766.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.385α = 90
b = 85.128β = 90
c = 108.561γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2005-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.8423EMBL/DESY, HAMBURGBW7B

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
11.5885.1399.60.05915.14.110698516.515
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)
11.581.6798.60.323.23.315300

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTBlue Laccase from Panus tigrinus (not yet deposited)1.5822.33106932101597533499.490.174670.173750.19215RANDOM19.701
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]
-0.18-0.450.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.774
r_dihedral_angle_4_deg18.958
r_dihedral_angle_3_deg11.094
r_dihedral_angle_1_deg6.151
r_scangle_it2.165
r_scbond_it1.504
r_angle_refined_deg1.382
r_mcangle_it1.004
r_mcbond_it0.585
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.774
r_dihedral_angle_4_deg18.958
r_dihedral_angle_3_deg11.094
r_dihedral_angle_1_deg6.151
r_scangle_it2.165
r_scbond_it1.504
r_angle_refined_deg1.382
r_mcangle_it1.004
r_mcbond_it0.585
r_nbtor_refined0.312
r_symmetry_vdw_refined0.224
r_nbd_refined0.209
r_symmetry_metal_ion_refined0.161
r_metal_ion_refined0.145
r_symmetry_hbond_refined0.141
r_chiral_restr0.13
r_xyhbond_nbd_refined0.11
r_bond_refined_d0.008
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3755
Nucleic Acid Atoms
Solvent Atoms548
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing