5ZRD

Tyrosinase from Burkholderia thailandensis (BtTYR) at low pH condition


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ZRE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.229322% (v/v) reagent alcohol, 100 mM sodium citrate dibasic, pH 4.2
Crystal Properties
Matthews coefficientSolvent content
3.1260.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.914α = 90
b = 142.914β = 90
c = 256.756γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702017-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.3123.897.80.0739.958.1131667
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.340.306

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 REPLACEMENTTHROUGHOUT5ZRE2.328.88124964667997.780.18190.17980.2211RANDOM47.944
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]
-0.91-0.45-0.912.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.673
r_dihedral_angle_4_deg17.643
r_dihedral_angle_3_deg17.372
r_dihedral_angle_1_deg7.474
r_angle_refined_deg1.596
r_angle_other_deg0.539
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.673
r_dihedral_angle_4_deg17.643
r_dihedral_angle_3_deg17.372
r_dihedral_angle_1_deg7.474
r_angle_refined_deg1.596
r_angle_other_deg0.539
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16544
Nucleic Acid Atoms
Solvent Atoms517
Heterogen Atoms148

Software

Software
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing