7R2U

CRYSTAL STRUCTURE OF AS-ISOLATED 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% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.6854.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.65α = 90
b = 127.65β = 90
c = 86.29γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MMirrors2021-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.99990DiamondI24

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
11.537.631000.1080.1210.0540.9968.3583956
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)
11.51.531001.3241.4810.6590.4311.25

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3ZIY1.537.6379820413499.970.10760.10540.1528RANDOM24.346
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]
1.410.711.41-4.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.14
r_dihedral_angle_4_deg21.359
r_dihedral_angle_3_deg13.403
r_dihedral_angle_1_deg7.11
r_rigid_bond_restr4.523
r_angle_refined_deg2.052
r_angle_other_deg0.691
r_chiral_restr0.131
r_bond_refined_d0.018
r_gen_planes_refined0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.14
r_dihedral_angle_4_deg21.359
r_dihedral_angle_3_deg13.403
r_dihedral_angle_1_deg7.11
r_rigid_bond_restr4.523
r_angle_refined_deg2.052
r_angle_other_deg0.691
r_chiral_restr0.131
r_bond_refined_d0.018
r_gen_planes_refined0.013
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3439
Nucleic Acid Atoms
Solvent Atoms639
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
AutoProcessphasing