2QPZ

Naphthalene 1,2-dioxygenase Rieske ferredoxin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP728236-38% PEG8000, 100 mM MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 282K
Crystal Properties
Matthews coefficientSolvent content
2.6854.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.23α = 90
b = 65.23β = 90
c = 49.44γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.934000ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.8558.599.60.0630.063814.210291
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.851.9597.50.2490.2492.97.71446

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1FQT1.8528.251026849399.480.1570.1540.197RANDOM24.734
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]
1.290.651.29-1.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.779
r_dihedral_angle_4_deg19.843
r_dihedral_angle_3_deg17.528
r_sphericity_free10.523
r_sphericity_bonded7.483
r_scangle_it6.619
r_dihedral_angle_1_deg6.552
r_scbond_it4.986
r_mcangle_it3.764
r_rigid_bond_restr3.342
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.779
r_dihedral_angle_4_deg19.843
r_dihedral_angle_3_deg17.528
r_sphericity_free10.523
r_sphericity_bonded7.483
r_scangle_it6.619
r_dihedral_angle_1_deg6.552
r_scbond_it4.986
r_mcangle_it3.764
r_rigid_bond_restr3.342
r_mcbond_it3.132
r_angle_refined_deg2.372
r_mcbond_other1.453
r_angle_other_deg1.309
r_xyhbond_nbd_refined0.338
r_nbd_other0.265
r_symmetry_hbond_refined0.265
r_nbd_refined0.249
r_symmetry_vdw_other0.204
r_nbtor_refined0.182
r_chiral_restr0.15
r_symmetry_vdw_refined0.099
r_nbtor_other0.094
r_bond_refined_d0.025
r_bond_other_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms818
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms4

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction