5NGX

The 1.06 A resolution structure of the L16G mutant of ferric cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitrite


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YL7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529850 mM sodium nitrite, 2.2 M ammonium sulphate and 0.1 M HEPES, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8656.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.91α = 90
b = 53.91β = 90
c = 183.21γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9282DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.0645.2496.80.0630.023113.17.7701688.53
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.061.08990.4930.5875.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2yl71.0645.2466609350696.70.17870.177580.20005RANDOM14.673
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]
0.640.320.64-2.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.577
r_sphericity_free24.608
r_dihedral_angle_4_deg14.306
r_dihedral_angle_3_deg11.838
r_sphericity_bonded8.705
r_rigid_bond_restr5.736
r_dihedral_angle_1_deg5.513
r_long_range_B_refined3.653
r_long_range_B_other3.651
r_angle_refined_deg2.179
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.577
r_sphericity_free24.608
r_dihedral_angle_4_deg14.306
r_dihedral_angle_3_deg11.838
r_sphericity_bonded8.705
r_rigid_bond_restr5.736
r_dihedral_angle_1_deg5.513
r_long_range_B_refined3.653
r_long_range_B_other3.651
r_angle_refined_deg2.179
r_scangle_other1.733
r_scbond_it1.49
r_scbond_other1.485
r_angle_other_deg1.457
r_mcangle_it1.384
r_mcangle_other1.384
r_mcbond_it1.05
r_mcbond_other1.044
r_chiral_restr0.083
r_gen_planes_refined0.017
r_bond_refined_d0.016
r_gen_planes_other0.011
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms945
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing