1UUW

NAPHTHALENE 1,2-DIOXYGENASE WITH NITRIC OXIDE 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
2.6253.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.556α = 90
b = 140.556β = 90
c = 210.288γ = 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 ID14-1ESRFID14-1

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
12.33092.70.0717.65.432084
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)
12.32.42950.2153.25.3

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 1EG92.33031759104191.90.1980.194RANDOM26.64
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]
0.220.110.22-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.976
r_dihedral_angle_1_deg4.443
r_scangle_it2.69
r_scbond_it1.587
r_angle_refined_deg1.434
r_mcangle_it1.203
r_angle_other_deg0.849
r_mcbond_it0.636
r_symmetry_hbond_refined0.36
r_nbd_refined0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.976
r_dihedral_angle_1_deg4.443
r_scangle_it2.69
r_scbond_it1.587
r_angle_refined_deg1.434
r_mcangle_it1.203
r_angle_other_deg0.849
r_mcbond_it0.636
r_symmetry_hbond_refined0.36
r_nbd_refined0.222
r_symmetry_vdw_other0.218
r_nbd_other0.208
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.142
r_chiral_restr0.087
r_metal_ion_refined0.042
r_xyhbond_nbd_other0.012
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
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 Atoms5088
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing