1O7G

NAPHTHALENE 1,2-DIOXYGENASE WITH NAPHTHALENE BOUND IN THE ACTIVE SITE.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EG9PDB ENTRY 1EG9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.5652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.67α = 90
b = 139.67β = 90
c = 208.109γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.72095.90.05911.35.4982025
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)
11.71.7397.50.19

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1EG91.72577908411795.90.1630.187RANDOM19.98
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]
0.530.270.53-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.971
r_dihedral_angle_1_deg5.361
r_scangle_it4.773
r_scbond_it2.977
r_mcangle_it1.982
r_angle_refined_deg1.811
r_symmetry_vdw_refined1.166
r_mcbond_it1.103
r_angle_other_deg0.847
r_symmetry_hbond_refined0.606
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.971
r_dihedral_angle_1_deg5.361
r_scangle_it4.773
r_scbond_it2.977
r_mcangle_it1.982
r_angle_refined_deg1.811
r_symmetry_vdw_refined1.166
r_mcbond_it1.103
r_angle_other_deg0.847
r_symmetry_hbond_refined0.606
r_xyhbond_nbd_other0.277
r_nbd_refined0.253
r_xyhbond_nbd_refined0.248
r_nbtor_other0.229
r_symmetry_vdw_other0.213
r_nbd_other0.21
r_chiral_restr0.118
r_bond_refined_d0.019
r_metal_ion_refined0.01
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5089
Nucleic Acid Atoms
Solvent Atoms519
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling