4FAS

Complex crystal structure of hydroxylamine oxidoreductase and NE1300 from Nitrosomonas europaea


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FGJMonomer of PDB ID: 1FGJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52920.1 M potassium nitrate, 0.1 M MES pH 7.5 and 46%(v/v) PEG 400, VAPOR DIFFUSION, temperature 292K
2VAPOR DIFFUSION7.52920.1 M potassium nitrate, 0.1 M MES pH 7.5 and 46%(v/v) PEG 400, VAPOR DIFFUSION, temperature 292K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.731α = 90
b = 142.618β = 90
c = 107.376γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirror2009-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97948APS19-ID

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
12.15086.70.1279.5544.6125826109103-332.67
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)
12.12.1469.30.5742.0363.94298

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMonomer of PDB ID: 1FGJ2.142.8911959395555507179.90.167010.167010.164930.20583RANDOM37.348
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]
-1.75-0.151.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.194
r_dihedral_angle_4_deg19.875
r_dihedral_angle_3_deg17.487
r_dihedral_angle_1_deg6.466
r_scangle_it4.39
r_scbond_it3.202
r_angle_refined_deg2.102
r_mcangle_it1.781
r_mcbond_it1.037
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.194
r_dihedral_angle_4_deg19.875
r_dihedral_angle_3_deg17.487
r_dihedral_angle_1_deg6.466
r_scangle_it4.39
r_scbond_it3.202
r_angle_refined_deg2.102
r_mcangle_it1.781
r_mcbond_it1.037
r_chiral_restr0.128
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13125
Nucleic Acid Atoms
Solvent Atoms785
Heterogen Atoms1279

Software

Software
Software NamePurpose
SBC-Collectdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling