6DAW

X-ray crystal structure of NapI L-arginine desaturase bound to Fe(II), L-arginine, and acetate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.5293potassium acetate, HEPES
Crystal Properties
Matthews coefficientSolvent content
2.2946.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.631α = 90
b = 121.631β = 90
c = 82.054γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.979APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.15099.60.1160.1220.0387.210.240215
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1499.70.9030.9510.2980.81610

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.15038124201699.360.20480.20260.2478RANDOM33.734
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]
-0.23-0.12-0.230.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.679
r_dihedral_angle_4_deg15.33
r_dihedral_angle_3_deg12.06
r_dihedral_angle_1_deg5.097
r_angle_refined_deg0.943
r_angle_other_deg0.701
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.679
r_dihedral_angle_4_deg15.33
r_dihedral_angle_3_deg12.06
r_dihedral_angle_1_deg5.097
r_angle_refined_deg0.943
r_angle_other_deg0.701
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5380
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms42

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing