1LS9

Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CTJPDB ENTRY 1CTJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62770.2 M Na-acetate, 0.1 M Na-cacodylate, pH 6.5, 30% w/v PEG 8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0840.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.063α = 90
b = 46.063β = 90
c = 100.526γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH165-mm MAR CCD2001-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8015EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.314.890698.40.05325.320.2527067
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.31.3297.60.3113.638.68

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1CTJ1.314.68425709135898.60.1570.149220.143390.19034RANDOM16.595
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]
0.48350.48350.0177
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor17.8
p_staggered_tor11.2
p_planar_tor5.3
p_scangle_it4.29
p_scbond_it3.384
p_mcangle_it2.8
p_mcbond_it2.405
p_multtor_nbd0.278
p_singtor_nbd0.165
p_chiral_restr0.138
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor17.8
p_staggered_tor11.2
p_planar_tor5.3
p_scangle_it4.29
p_scbond_it3.384
p_mcangle_it2.8
p_mcbond_it2.405
p_multtor_nbd0.278
p_singtor_nbd0.165
p_chiral_restr0.138
p_xyhbond_nbd0.071
p_hb_or_metal_coord0.059
p_planar_d0.035
p_angle_d0.033
p_bond_d0.024
p_plane_restr0.016
o_bond_d_na
o_bond_d_prot
p_xhyhbond_nbd
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms674
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms43

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement