3EHB | pdb_00003ehb

A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AR1PDB ENTRY 1AR1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.3291MPEG 2000 is contained in the crystallization buffer pH 5.5, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
4.170.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.461α = 90
b = 151.332β = 90
c = 157.487γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.92021SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.322098.80.0919.148714687146-3-351.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.322.4973.938161

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1AR12.3219.69-3868538423026231000.206180.206180.205050.20370.24240.2049RANDOM60.153
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_deg37.705
r_dihedral_angle_4_deg25.498
r_dihedral_angle_3_deg19.058
r_dihedral_angle_1_deg7.709
r_mcangle_it5.882
r_scangle_it5.773
r_mcbond_it4.385
r_scbond_it4.243
r_angle_refined_deg2.488
r_nbtor_refined0.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.705
r_dihedral_angle_4_deg25.498
r_dihedral_angle_3_deg19.058
r_dihedral_angle_1_deg7.709
r_mcangle_it5.882
r_scangle_it5.773
r_mcbond_it4.385
r_scbond_it4.243
r_angle_refined_deg2.488
r_nbtor_refined0.326
r_symmetry_vdw_refined0.277
r_nbd_refined0.251
r_xyhbond_nbd_refined0.197
r_metal_ion_refined0.184
r_chiral_restr0.182
r_symmetry_hbond_refined0.05
r_bond_refined_d0.027
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7954
Nucleic Acid Atoms
Solvent Atoms379
Heterogen Atoms703

Software

Software
Software NamePurpose
SBC-Collectdata collection
DMmodel building
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
DMphasing