1O7H

NAPHTHALENE 1,2-DIOXYGENASE WITH OXIDIZED RIESKE IRON SULPHUR CENTER 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 = 138.308α = 90
b = 138.308β = 90
c = 206.67γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCHESS 80MM1999-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.230980.074164.1837958
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)
12.22.2598.60.363

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 1EG92.23036554192599.40.2080.242RANDOM22.83
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]
0.20.10.2-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.4
r_dihedral_angle_1_deg4.19
r_scangle_it3.639
r_scbond_it2.295
r_angle_refined_deg1.522
r_mcangle_it1.493
r_mcbond_it0.806
r_symmetry_hbond_refined0.559
r_nbd_refined0.227
r_symmetry_vdw_refined0.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.4
r_dihedral_angle_1_deg4.19
r_scangle_it3.639
r_scbond_it2.295
r_angle_refined_deg1.522
r_mcangle_it1.493
r_mcbond_it0.806
r_symmetry_hbond_refined0.559
r_nbd_refined0.227
r_symmetry_vdw_refined0.205
r_xyhbond_nbd_refined0.151
r_chiral_restr0.102
r_metal_ion_refined0.073
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
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_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 Atoms358
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling