2HMM

Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Anthracene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O7H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5279.151.9-2.2 M Ammonium Sulfate, 4-6% Dioxane, 0.1 M MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.15K
Crystal Properties
Matthews coefficientSolvent content
2.6954.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.725α = 90
b = 139.725β = 90
c = 208.113γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12004-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.04021ALS4.2.2

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
11.615.9798.50.069103.16100884100884
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)
1.61.6695.50.4492.32.949731

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRIGID BODY REFINEMENTTHROUGHOUT1O7H1.615.97100819100819504998.290.1650.1650.1640.198RANDOM16.738
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]
0.480.240.48-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.222
r_dihedral_angle_4_deg18.333
r_dihedral_angle_3_deg13.426
r_sphericity_free9.64
r_dihedral_angle_1_deg6.489
r_scangle_it3.194
r_scbond_it2.588
r_rigid_bond_restr2.222
r_sphericity_bonded2.143
r_mcangle_it1.475
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.222
r_dihedral_angle_4_deg18.333
r_dihedral_angle_3_deg13.426
r_sphericity_free9.64
r_dihedral_angle_1_deg6.489
r_scangle_it3.194
r_scbond_it2.588
r_rigid_bond_restr2.222
r_sphericity_bonded2.143
r_mcangle_it1.475
r_angle_refined_deg1.422
r_mcbond_it1.262
r_angle_other_deg0.898
r_mcbond_other0.333
r_symmetry_vdw_other0.242
r_nbd_other0.212
r_nbd_refined0.211
r_symmetry_vdw_refined0.191
r_nbtor_refined0.181
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.144
r_nbtor_other0.088
r_chiral_restr0.083
r_metal_ion_refined0.021
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5088
Nucleic Acid Atoms
Solvent Atoms731
Heterogen Atoms131

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction