2JIO

A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NAPPDB ENTRY 2NAP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.1M MES, PH 6.0, 6% PEG 8000 AS PURIFIED PROTEIN ONLY
Crystal Properties
Matthews coefficientSolvent content
2.3955.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.188α = 90
b = 106.188β = 90
c = 135.13γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.27699.50.1627.134.5450242
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)
12.22.3298.61.213.335

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 DIFFRACTIONSADTHROUGHOUTPDB ENTRY 2NAP2.292.0642713226799.40.1530.150.209RANDOM36.15
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]
-2.29-1.15-2.293.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.337
r_dihedral_angle_4_deg21.084
r_dihedral_angle_3_deg15.868
r_dihedral_angle_1_deg6.648
r_scangle_it2.764
r_scbond_it1.968
r_angle_refined_deg1.62
r_mcangle_it1.012
r_mcbond_it0.634
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.337
r_dihedral_angle_4_deg21.084
r_dihedral_angle_3_deg15.868
r_dihedral_angle_1_deg6.648
r_scangle_it2.764
r_scbond_it1.968
r_angle_refined_deg1.62
r_mcangle_it1.012
r_mcbond_it0.634
r_nbtor_refined0.305
r_symmetry_hbond_refined0.212
r_nbd_refined0.203
r_xyhbond_nbd_refined0.182
r_symmetry_vdw_refined0.152
r_chiral_restr0.111
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5622
Nucleic Acid Atoms
Solvent Atoms810
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing