2JIM

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
16COCRYSTALLISATION WITH 10MM OF NAN3 (AZIDE) IN 200MM OF DDNAPA (IE PROTEIN) WHICH HAD BEEN REDUCED BY DITHIONITE IN ANAEROBIC CONDITIONS AND THEN AIR REOXIDISED BEFORE SETTTING UP FOR CRYSTALLISATIONS STRAIGHT AFTER THAWING FROM 193K. CRYSTALLISATION CONDITION 0.1M MES PH 6.0, 8% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.5150.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.307α = 90
b = 106.307β = 90
c = 133.558γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.4554.0799.90.1318.19.8326491
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)
12.452.5899.81.1615.8

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 2NAP2.4592.0631238130099.70.1810.1780.252RANDOM47.87
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]
-2.39-1.2-2.393.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.749
r_dihedral_angle_4_deg23.346
r_dihedral_angle_3_deg18.121
r_dihedral_angle_1_deg6.758
r_scangle_it2.911
r_scbond_it1.858
r_angle_refined_deg1.67
r_mcangle_it1.079
r_mcbond_it0.633
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.749
r_dihedral_angle_4_deg23.346
r_dihedral_angle_3_deg18.121
r_dihedral_angle_1_deg6.758
r_scangle_it2.911
r_scbond_it1.858
r_angle_refined_deg1.67
r_mcangle_it1.079
r_mcbond_it0.633
r_nbtor_refined0.317
r_symmetry_hbond_refined0.283
r_nbd_refined0.22
r_xyhbond_nbd_refined0.213
r_symmetry_vdw_refined0.168
r_chiral_restr0.112
r_bond_refined_d0.015
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 Atoms453
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
REFMACphasing