3O5A

Crystal Structure of partially reduced Periplasmic Nitrate Reductase from Cupriavidus necator using Ionic Liquids


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729315% PEG 3350, 0.2M sodium formate, 0.4M [C4MIM]Cl-, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.4α = 90
b = 71.41β = 121.04
c = 128.41γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7228.3499.61743.5130188978954935
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.8199.6174

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2NAP1.7227.6315435093004488999.620.14350.144730.142780.1815RANDOM12.375
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]
-0.09-0.040.07-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.44
r_dihedral_angle_4_deg18.611
r_dihedral_angle_3_deg13.8
r_dihedral_angle_1_deg8.731
r_scangle_it4.383
r_scbond_it2.971
r_angle_refined_deg2.31
r_mcangle_it1.936
r_mcbond_it1.289
r_chiral_restr0.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.44
r_dihedral_angle_4_deg18.611
r_dihedral_angle_3_deg13.8
r_dihedral_angle_1_deg8.731
r_scangle_it4.383
r_scbond_it2.971
r_angle_refined_deg2.31
r_mcangle_it1.936
r_mcbond_it1.289
r_chiral_restr0.198
r_bond_refined_d0.028
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7121
Nucleic Acid Atoms
Solvent Atoms787
Heterogen Atoms248

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling