2Y9W | pdb_00002y9w

Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JS8PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1
experimental modelPDB 1LNLPDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1
experimental modelPDB 1WX2PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1
experimental modelPDB 1BT1PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.610% PEG 4000, 100 MM NA ACETATE PH 4.6, 5 MM HOLMIUM CHLORIDE.
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.06α = 90
b = 104.52β = 90
c = 109.05γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.361.11000.127.73.75381332.6
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)
12.32.421000.552.33.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT12.347.135036626991000.1840.1810.180.2370.24RANDOM33.27
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]
-0.07-0.010.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.451
r_dihedral_angle_3_deg15.705
r_dihedral_angle_4_deg13.663
r_dihedral_angle_1_deg5.999
r_scangle_it2.197
r_scbond_it1.576
r_angle_refined_deg1.164
r_mcangle_it0.845
r_mcbond_it0.437
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.451
r_dihedral_angle_3_deg15.705
r_dihedral_angle_4_deg13.663
r_dihedral_angle_1_deg5.999
r_scangle_it2.197
r_scbond_it1.576
r_angle_refined_deg1.164
r_mcangle_it0.845
r_mcbond_it0.437
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms8518
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing