9IKI | pdb_00009iki

Bovine Heart Cytochrome c Oxidase in the Nitrous Oxide-bound Fully Reduced State


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8H8S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.827740 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
Crystal Properties
Matthews coefficientSolvent content
4.0269.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.9α = 90
b = 204β = 90
c = 177.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS EIGER X 16M2023-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.752001000.118122.214128807831.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.899.90.3940.7481.2514

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT8H8S1.75406247713277399.970.154780.152970.16540.189020.198RANDOM39.829
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]
-2.768.13-5.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.409
r_dihedral_angle_4_deg16.61
r_dihedral_angle_3_deg14.082
r_dihedral_angle_1_deg6.294
r_scangle_other5.203
r_long_range_B_refined4.987
r_long_range_B_other4.955
r_scbond_it4.612
r_scbond_other4.612
r_mcangle_it3.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.409
r_dihedral_angle_4_deg16.61
r_dihedral_angle_3_deg14.082
r_dihedral_angle_1_deg6.294
r_scangle_other5.203
r_long_range_B_refined4.987
r_long_range_B_other4.955
r_scbond_it4.612
r_scbond_other4.612
r_mcangle_it3.856
r_mcangle_other3.856
r_rigid_bond_restr3.831
r_mcbond_it3.407
r_mcbond_other3.407
r_angle_refined_deg2.056
r_angle_other_deg1.471
r_chiral_restr0.453
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_gen_planes_other0.006
r_bond_other_d0.002
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms27834
Nucleic Acid Atoms
Solvent Atoms2001
Heterogen Atoms2592

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing