6AIO

Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseudomonas putida DLL-E4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29310% isopropanol, 0.1M Tris-HCl, pH 8.5, 13.5 % (w/v) PEG 4000, 5% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.2946.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.845α = 90
b = 76.323β = 90
c = 208.25γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1.5397SSRFBL17U

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
12.043099.10.05225.095.955036
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.042.110.095

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 REPLACEMENTTHROUGHOUT3IHG2.043052274268898.970.175320.173190.21705RANDOM22.807
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]
0.72-0.02-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.627
r_dihedral_angle_4_deg17.301
r_dihedral_angle_3_deg16.642
r_long_range_B_refined7.497
r_long_range_B_other7.448
r_dihedral_angle_1_deg6.628
r_scangle_other4.999
r_scbond_it3.255
r_scbond_other3.255
r_mcangle_it2.992
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.627
r_dihedral_angle_4_deg17.301
r_dihedral_angle_3_deg16.642
r_long_range_B_refined7.497
r_long_range_B_other7.448
r_dihedral_angle_1_deg6.628
r_scangle_other4.999
r_scbond_it3.255
r_scbond_other3.255
r_mcangle_it2.992
r_mcangle_other2.991
r_mcbond_it2.048
r_mcbond_other2.047
r_angle_refined_deg1.84
r_angle_other_deg1.29
r_chiral_restr0.111
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.006
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 Atoms6094
Nucleic Acid Atoms
Solvent Atoms619
Heterogen Atoms

Software

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