2EI0

Anaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexed with 3,4-dihydroxybiphenyl


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72941.8M NaCl, 0.1M MgCl2, 0.1M Hepes, anaerobic crystallization, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.1160.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.87α = 90
b = 117.87β = 90
c = 121.594γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2001-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.99APS19-BM

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
11.6501000.0568.949031
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)
11.699.90.738

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 REPLACEMENTTHROUGHOUT1HAN1.649.1549031262291.380.160590.159780.17562RANDOM14.069
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]
0.040.04-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.867
r_dihedral_angle_4_deg17.273
r_dihedral_angle_3_deg11.445
r_dihedral_angle_1_deg5.862
r_scangle_it2.355
r_scbond_it1.527
r_angle_refined_deg1.169
r_mcangle_it0.967
r_mcbond_it0.636
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.867
r_dihedral_angle_4_deg17.273
r_dihedral_angle_3_deg11.445
r_dihedral_angle_1_deg5.862
r_scangle_it2.355
r_scbond_it1.527
r_angle_refined_deg1.169
r_mcangle_it0.967
r_mcbond_it0.636
r_nbtor_refined0.311
r_nbd_refined0.192
r_symmetry_vdw_refined0.154
r_symmetry_hbond_refined0.135
r_xyhbond_nbd_refined0.121
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2274
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms50

Software

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