4EIC

Crystal structure of reduced cytochrome c6 from Synechococcus sp. PCC 7002 at ultra-high resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DR0PDB ENTRY 3DR0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52922.2M Ammonium sulphate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.0239.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.86α = 90
b = 27.69β = 101.1
c = 44.07γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8166EMBL/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
10.8432.5594.80.06315.2166490864908-39.45
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)
10.840.8680.60.5073.234.34069

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 REPLACEMENTFREE RPDB ENTRY 3DR00.8432.55649086490897494.80.10580.10580.10560.1271RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
12664.26800.71
RMS Deviations
KeyRefinement Restraint Deviation
s_zero_chiral_vol0.115
s_anti_bump_dis_restr0.093
s_approx_iso_adps0.08
s_angle_d0.057
s_bond_d0.026
s_similar_adp_cmpnt0.025
s_rigid_bond_adp_cmpnt0.005
s_from_restr_planes0.0039
s_similar_dist
s_non_zero_chiral_vol
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms662
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms55

Software

Software
Software NamePurpose
AUTOMARdata collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling