6RRP

Crystal structure of tyrosinase PvdP from Pseudomonas aeruginosa bound to copper and phenylthiourea


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6RRR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529120% PEG 3350, 0.1M Bis-Tris Propane
Crystal Properties
Matthews coefficientSolvent content
2.6453.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.239α = 90
b = 113.88β = 94.34
c = 100.577γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FKB2017-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.0332PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.45099.40.0840.0970.0490.99710.93.844062
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4996.40.6080.7080.3590.8413.8

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 REPLACEMENTTHROUGHOUT6RRR2.449.5641702233699.380.19820.19490.2544RANDOM44.657
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]
6.44-1.65-2.35-3.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.732
r_dihedral_angle_4_deg16.728
r_dihedral_angle_3_deg16.453
r_dihedral_angle_1_deg7.874
r_angle_refined_deg1.579
r_angle_other_deg1.521
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.732
r_dihedral_angle_4_deg16.728
r_dihedral_angle_3_deg16.453
r_dihedral_angle_1_deg7.874
r_angle_refined_deg1.579
r_angle_other_deg1.521
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7445
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction