6JU1

p-Hydroxybenzoate hydroxylase Y385F mutant complexed with 3,4-dihydroxybenzoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IUV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.150.15 M KBr, 30% PEG 2000 monomethyl ether
Crystal Properties
Matthews coefficientSolvent content
2.448.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.866α = 90
b = 145.901β = 90
c = 86.421γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2018-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.29Photon FactoryAR-NW12A

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
11.65099.60.10328.112.459096
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.63930.9140.7511.37.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1IUV1.640.1356131294199.540.159450.158030.18594RANDOM23.047
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.803
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg13.685
r_dihedral_angle_1_deg6.634
r_long_range_B_refined6.443
r_long_range_B_other6.315
r_scangle_other4.809
r_scbond_it3.184
r_scbond_other3.184
r_mcangle_other2.651
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.803
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg13.685
r_dihedral_angle_1_deg6.634
r_long_range_B_refined6.443
r_long_range_B_other6.315
r_scangle_other4.809
r_scbond_it3.184
r_scbond_other3.184
r_mcangle_other2.651
r_mcangle_it2.646
r_mcbond_it1.952
r_mcbond_other1.927
r_angle_refined_deg1.759
r_angle_other_deg1.483
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3116
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms125

Software

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