1NDO

NAPHTHALENE 1,2-DIOXYGENASE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.9759

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105α = 90
b = 174β = 90
c = 282.5γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1997-11-06M
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
12.253095.50.09114.666.211706729.5
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)
2.252.2996.90.3863.64

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMIR AND MADTHROUGHOUT2.2530122414790.220.190.24RANDOM34.9
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]
4-6.32.3
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor26.6
p_staggered_tor18.2
p_planar_tor9.6
p_scangle_it7.9
p_scbond_it6.5
p_mcangle_it3.7
p_mcbond_it2.7
p_multtor_nbd0.25
p_xyhbond_nbd0.21
p_singtor_nbd0.19
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor26.6
p_staggered_tor18.2
p_planar_tor9.6
p_scangle_it7.9
p_scbond_it6.5
p_mcangle_it3.7
p_mcbond_it2.7
p_multtor_nbd0.25
p_xyhbond_nbd0.21
p_singtor_nbd0.19
p_chiral_restr0.16
p_planar_d0.06
p_angle_d0.04
p_plane_restr0.04
p_bond_d0.02
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15270
Nucleic Acid Atoms
Solvent Atoms2040
Heterogen Atoms15

Software

Software
Software NamePurpose
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling