3SBR

Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form with substrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FWXPDB entry 1FWX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729816 % PEG 6000, 0.2 M imidazole/malate buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.577α = 111.45
b = 106.453β = 107.22
c = 130.876γ = 90.72
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6Mmirrors2010-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

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
12.2495.0594.60.0912.83.820599519487222

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 REPLACEMENTTHROUGHOUTPDB entry 1FWX2.24951948721029993.270.175840.173170.22655RANDOM20.219
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]
0.13-0.09-0.03-0.13-0.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.771
r_dihedral_angle_4_deg16.969
r_dihedral_angle_3_deg16.055
r_dihedral_angle_1_deg7.045
r_scangle_it2.539
r_scbond_it1.556
r_angle_refined_deg1.317
r_mcangle_it0.909
r_mcbond_it0.474
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.771
r_dihedral_angle_4_deg16.969
r_dihedral_angle_3_deg16.055
r_dihedral_angle_1_deg7.045
r_scangle_it2.539
r_scbond_it1.556
r_angle_refined_deg1.317
r_mcangle_it0.909
r_mcbond_it0.474
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms36623
Nucleic Acid Atoms
Solvent Atoms2628
Heterogen Atoms124

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling