6GT0

Nitrite-bound copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293.151.2 M ammonium sulphate, 100 mM citrate buffer, pH 5.0
Crystal Properties
Matthews coefficientSolvent content
1.9637.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.92α = 90
b = 94.92β = 90
c = 94.92γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225-HS2017-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.242SACLABL2

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965)Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965)SACLA goniometer3.4 M Na-malonate, pH 5.0 and 100 mM NaNO2.
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
11030
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
1103912571257

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Split (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
11.554.861000.1066.6154.74584622.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.541000.8532.350.8

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 DIFFRACTIONTHROUGHOUT1.554.8643498229599.990.144810.143430.17053RANDOM19.23
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.831
r_dihedral_angle_4_deg21.782
r_dihedral_angle_1_deg21.215
r_dihedral_angle_3_deg12.809
r_long_range_B_refined4.666
r_long_range_B_other4.323
r_scangle_other3.584
r_scbond_it2.524
r_scbond_other2.472
r_mcangle_it1.852
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.831
r_dihedral_angle_4_deg21.782
r_dihedral_angle_1_deg21.215
r_dihedral_angle_3_deg12.809
r_long_range_B_refined4.666
r_long_range_B_other4.323
r_scangle_other3.584
r_scbond_it2.524
r_scbond_other2.472
r_mcangle_it1.852
r_mcangle_other1.851
r_angle_refined_deg1.594
r_mcbond_it1.289
r_mcbond_other1.287
r_angle_other_deg1.053
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2574
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms31

Software

Software
Software NamePurpose
CrystFELdata reduction
REFMACrefinement