9FUK | pdb_00009fuk

CRYSTAL STRUCTURE OF NITRIC OXIDE-TREATED Q262N 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% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.856.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.069α = 90
b = 128.069β = 90
c = 86.352γ = 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 I030.97625DiamondI03

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
11.0937.7487.20.0460.0550.030.9999.22.5216270
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)
11.141.1682.90.9071.1430.6840.3741.9

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 SYNTHESISTHROUGHOUT1.0937.742162701097598.1460.1070.10660.10660.12230.1222RANDOM15.283
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]
-0.127-0.063-0.1270.412
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it17.705
r_dihedral_angle_6_deg15.835
r_lrange_other12.457
r_dihedral_angle_3_deg11.149
r_dihedral_angle_2_deg8.715
r_dihedral_angle_1_deg7.063
r_scangle_it6.345
r_scangle_other6.345
r_mcangle_other4.54
r_mcangle_it4.531
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it17.705
r_dihedral_angle_6_deg15.835
r_lrange_other12.457
r_dihedral_angle_3_deg11.149
r_dihedral_angle_2_deg8.715
r_dihedral_angle_1_deg7.063
r_scangle_it6.345
r_scangle_other6.345
r_mcangle_other4.54
r_mcangle_it4.531
r_scbond_other4.349
r_scbond_it4.348
r_mcbond_it3.095
r_mcbond_other3.069
r_rigid_bond_restr2.967
r_angle_refined_deg1.775
r_angle_other_deg0.632
r_symmetry_xyhbond_nbd_refined0.251
r_symmetry_nbd_refined0.248
r_nbd_other0.233
r_nbd_refined0.225
r_xyhbond_nbd_refined0.221
r_symmetry_nbd_other0.196
r_nbtor_refined0.176
r_metal_ion_refined0.133
r_chiral_restr0.098
r_symmetry_xyhbond_nbd_other0.087
r_symmetry_nbtor_other0.086
r_symmetry_metal_ion_refined0.073
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3428
Nucleic Acid Atoms
Solvent Atoms821
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
Cootmodel building
REFMACphasing