2HML

Crystal Structure of the Naphthalene 1,2-Dioxygenase F352V Mutant Bound to Phenanthrene.


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
2.754.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.865α = 90
b = 139.865β = 90
c = 208.431γ = 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
11.817.9799.90.1089.44.667238172381
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)
11.81.861000.4643.14.647201

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 REFINEMENTTHROUGHOUT1O7H1.817.977235972359365199.740.1650.1650.1640.19RANDOM15.758
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]
0.350.180.35-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.986
r_dihedral_angle_4_deg17.153
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg6.381
r_scangle_it2.638
r_scbond_it1.756
r_angle_refined_deg1.322
r_mcangle_it1.047
r_mcbond_it0.907
r_angle_other_deg0.877
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.986
r_dihedral_angle_4_deg17.153
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg6.381
r_scangle_it2.638
r_scbond_it1.756
r_angle_refined_deg1.322
r_mcangle_it1.047
r_mcbond_it0.907
r_angle_other_deg0.877
r_metal_ion_refined0.3
r_symmetry_vdw_other0.243
r_nbd_refined0.21
r_nbd_other0.202
r_nbtor_refined0.178
r_symmetry_hbond_refined0.161
r_mcbond_other0.151
r_symmetry_vdw_refined0.129
r_xyhbond_nbd_refined0.125
r_nbtor_other0.086
r_chiral_restr0.077
r_bond_refined_d0.01
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 Atoms5069
Nucleic Acid Atoms
Solvent Atoms550
Heterogen Atoms112

Software

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