8WEQ

p-hydroxybenzoate 3-monooxygenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.150.2M Magnesium chloride hexahydrate, 10% (v/v) Ethylene glycol, 0.1M HEPES pH 7.5, 15% (v/v) PEG Smear Medium, 5% (v/v) 2-Propanol
Crystal Properties
Matthews coefficientSolvent content
3.2562.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.74α = 90
b = 178.03β = 116.167
c = 89.13γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray125PIXELDECTRIS PILATUS3 6M2022-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 11C0.97942PAL/PLS11C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
13.2929.90196.940.99714.196.833249
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.293.4080.861

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3.2929.90133249166396.9420.1990.19550.255875.42
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]
5.1630.685-2.78-2.061
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.03
r_dihedral_angle_4_deg17.243
r_dihedral_angle_3_deg16.65
r_lrange_other8.212
r_lrange_it8.211
r_scangle_it7.615
r_scangle_other7.615
r_dihedral_angle_1_deg6.198
r_mcangle_other5.893
r_mcangle_it5.891
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.03
r_dihedral_angle_4_deg17.243
r_dihedral_angle_3_deg16.65
r_lrange_other8.212
r_lrange_it8.211
r_scangle_it7.615
r_scangle_other7.615
r_dihedral_angle_1_deg6.198
r_mcangle_other5.893
r_mcangle_it5.891
r_scbond_it5.423
r_scbond_other5.423
r_mcbond_it3.936
r_mcbond_other3.933
r_angle_other_deg2.374
r_angle_refined_deg1.908
r_nbd_other0.375
r_symmetry_nbd_other0.271
r_nbd_refined0.243
r_xyhbond_nbd_refined0.215
r_nbtor_refined0.205
r_symmetry_nbd_refined0.181
r_symmetry_xyhbond_nbd_other0.125
r_chiral_restr0.102
r_symmetry_nbtor_other0.083
r_bond_other_d0.036
r_bond_refined_d0.016
r_gen_planes_other0.015
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12444
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms159

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing