1O7W

NAPHTHALENE 1,2-DIOXYGENASE, FULLY REDUCED FORM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NDOPDB ENTRY 1NDO

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 = 139.526α = 90
b = 139.526β = 90
c = 208.103γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR1999-10-15MSINGLE 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
11.95094.40.06110.56.357814
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)
11.91.9796.60.2332.14.5

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 1NDO1.93054884292194.40.1810.208RANDOM26.01
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]
0.490.250.49-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.034
r_dihedral_angle_1_deg5.813
r_scangle_it3.768
r_scbond_it2.236
r_mcangle_it1.489
r_angle_refined_deg1.433
r_angle_other_deg1.043
r_mcbond_it0.76
r_nbd_refined0.212
r_nbd_other0.201
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.034
r_dihedral_angle_1_deg5.813
r_scangle_it3.768
r_scbond_it2.236
r_mcangle_it1.489
r_angle_refined_deg1.433
r_angle_other_deg1.043
r_mcbond_it0.76
r_nbd_refined0.212
r_nbd_other0.201
r_symmetry_vdw_other0.201
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.123
r_chiral_restr0.101
r_symmetry_hbond_refined0.077
r_bond_refined_d0.012
r_xyhbond_nbd_other0.01
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_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 Atoms5088
Nucleic Acid Atoms
Solvent Atoms378
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing