9FUI | pdb_00009fui

CRYSTAL STRUCTURE OF NITRIC OXIDE TREATED F295L MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZIY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.7277100 mM bis-tris propane pH 7.7, 200 mM sodium citrate, and 22% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.7455.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.275α = 90
b = 128.275β = 90
c = 86.348γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.86999DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.1737.05797.20.0630.070.0320.99910.34.7173732
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)
11.171.1973.20.8531.0430.5880.50412.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.1737.057173704858997.1740.1060.10520.10520.12740.1274RANDOM16.042
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]
0.1110.0560.111-0.362
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it19.226
r_dihedral_angle_6_deg16.125
r_lrange_other13.622
r_dihedral_angle_3_deg11.142
r_dihedral_angle_2_deg8.199
r_dihedral_angle_1_deg7.02
r_scangle_it6.684
r_scangle_other6.684
r_mcangle_other4.772
r_mcangle_it4.771
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it19.226
r_dihedral_angle_6_deg16.125
r_lrange_other13.622
r_dihedral_angle_3_deg11.142
r_dihedral_angle_2_deg8.199
r_dihedral_angle_1_deg7.02
r_scangle_it6.684
r_scangle_other6.684
r_mcangle_other4.772
r_mcangle_it4.771
r_scbond_other4.735
r_scbond_it4.734
r_mcbond_it3.394
r_rigid_bond_restr3.369
r_mcbond_other3.364
r_angle_refined_deg1.804
r_angle_other_deg0.68
r_symmetry_xyhbond_nbd_refined0.271
r_nbd_refined0.259
r_nbd_other0.216
r_symmetry_nbd_refined0.215
r_xyhbond_nbd_refined0.212
r_symmetry_nbd_other0.193
r_nbtor_refined0.175
r_chiral_restr0.098
r_symmetry_nbtor_other0.085
r_gen_planes_refined0.012
r_bond_refined_d0.011
r_gen_planes_other0.007
r_metal_ion_refined0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3437
Nucleic Acid Atoms
Solvent Atoms775
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
Cootmodel building
REFMACphasing