4EIE

Crystal structure of cytochrome c6C from Synechococcus sp. PCC 7002


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5292Protein solution: 15 mg/ml cytochrome c6C in 0.1 M TRIS pH 7.5, 0.2 M NaCl and 1 mM PMSF; Precipitant solution: 2 M NaCl and 2 M (NH4)2SO4. pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.0840.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.13α = 90
b = 56.13β = 90
c = 49.64γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANELmirrors2010-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8149EMBL/DESY, HAMBURGX11

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
11.0321.0499.30.08821.823.43953239532-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.031.091000.8322.913.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.0319.843848838488101799.230.136710.136020.16344RANDOM9.113
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]
-0.07-0.070.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.742
r_dihedral_angle_3_deg10.648
r_dihedral_angle_4_deg8.953
r_dihedral_angle_1_deg5.711
r_scangle_it4.395
r_scbond_it3.146
r_mcangle_it2.567
r_angle_refined_deg1.898
r_mcbond_it1.816
r_rigid_bond_restr1.373
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.742
r_dihedral_angle_3_deg10.648
r_dihedral_angle_4_deg8.953
r_dihedral_angle_1_deg5.711
r_scangle_it4.395
r_scbond_it3.146
r_mcangle_it2.567
r_angle_refined_deg1.898
r_mcbond_it1.816
r_rigid_bond_restr1.373
r_angle_other_deg1.223
r_mcbond_other0.617
r_chiral_restr0.139
r_bond_refined_d0.021
r_gen_planes_refined0.014
r_bond_other_d0.002
r_gen_planes_other0.002
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms621
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms51

Software

Software
Software NamePurpose
AUTOMARdata collection
Auto-Rickshawphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling