8R2S

Heme-dependent l-tyrosine hydroxylase (TyrH) from Streptomyces sclerotialus: fourfold mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KQU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52931 M imidazole/Mes monohydrate, 0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 sodium citrate tribasic dihydrate, 0.2 M sodium potassium tartrate tetrahydrate, 0.2 M sodium oxamate
Crystal Properties
Matthews coefficientSolvent content
2.1943.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.61α = 90
b = 74.834β = 90
c = 156.906γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2023-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.873130ESRFMASSIF-1

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
12.7156.9199.90.1870.2210.0870.9877.16.417405
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)
12.72.831000.7990.8720.3450.7656.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.778.451649186899.850.211320.207550.28663RANDOM39.87
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]
1.58-1.15-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.779
r_dihedral_angle_4_deg20.896
r_dihedral_angle_3_deg17.004
r_long_range_B_refined9.014
r_long_range_B_other9.013
r_dihedral_angle_1_deg7.644
r_scangle_other5.885
r_mcangle_it5.608
r_mcangle_other5.607
r_scbond_it3.786
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.779
r_dihedral_angle_4_deg20.896
r_dihedral_angle_3_deg17.004
r_long_range_B_refined9.014
r_long_range_B_other9.013
r_dihedral_angle_1_deg7.644
r_scangle_other5.885
r_mcangle_it5.608
r_mcangle_other5.607
r_scbond_it3.786
r_scbond_other3.785
r_mcbond_it3.65
r_mcbond_other3.648
r_angle_refined_deg1.68
r_angle_other_deg1.263
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4247
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms105

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing