2ZT9

Crystal Structure of the Cytochrome b6f Complex from Nostoc sp. PCC 7120


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E74 

Crystallization

Crystal Properties
Matthews coefficientSolvent content
6.02985179.601486

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.225α = 90
b = 159.225β = 90
c = 365.886γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
1398.30.085.454614-3

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 REPLACEMENTTHROUGHOUT2E74345.6951833277098.510.231420.229960.25908RANDOM73.68
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]
-0.19-0.1-0.190.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.904
r_dihedral_angle_3_deg19.968
r_dihedral_angle_4_deg16.704
r_dihedral_angle_1_deg5.831
r_angle_refined_deg1.792
r_scangle_it1.717
r_scbond_it0.986
r_mcangle_it0.946
r_mcbond_it0.528
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.904
r_dihedral_angle_3_deg19.968
r_dihedral_angle_4_deg16.704
r_dihedral_angle_1_deg5.831
r_angle_refined_deg1.792
r_scangle_it1.717
r_scbond_it0.986
r_mcangle_it0.946
r_mcbond_it0.528
r_nbtor_refined0.31
r_nbd_refined0.226
r_metal_ion_refined0.209
r_symmetry_vdw_refined0.186
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.141
r_chiral_restr0.13
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 Atoms7364
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms545

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling