6JU9

Aspergillus oryzae active-tyrosinase copper-bound C92A mutant complexed with L-tyrosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3W6W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229320% polyethylene glycol (PEG) 3350, 30mM NH4NO3
Crystal Properties
Matthews coefficientSolvent content
2.0740.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.544α = 90
b = 104.97β = 90
c = 154.877γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2015-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900SPring-8BL44XU

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
11.425097.90.08719.27164029
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)
11.421.44960.395.27

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 REPLACEMENTFREE R-VALUE3W6W1.42301639358126980.1560.15390.1967RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
337709.1
RMS Deviations
KeyRefinement Restraint Deviation
s_from_restr_planes0.3765
s_non_zero_chiral_vol0.0628
s_zero_chiral_vol0.0616
s_similar_adp_cmpnt0.0428
s_rigid_bond_adp_cmpnt0.0266
s_angle_d0.0193
s_bond_d0.0063
s_similar_dist
s_anti_bump_dis_restr
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7002
Nucleic Acid Atoms
Solvent Atoms759
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
SHELXLrefinement