1E84

Cytochrome c' from Alcaligenes xylosoxidans - reduced structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CGOPDB ENTRY 1CGO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5. REDUCED USING MOTHER LIQUOR CONTAINING 20 MM SODIUM DITHIONITE.
Crystal Properties
Matthews coefficientSolvent content
2.7154.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.819α = 90
b = 52.819β = 90
c = 182.602γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUMMIRRORS2000-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.94097.10.04131.64.912387-322
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)
11.91.9384.50.1228.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1CGO1.9401238759797.10.2170.273RANDOM22
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
p_transverse_tor27.5
p_staggered_tor13.7
p_scangle_it6.156
p_scbond_it5.516
p_planar_tor5
p_mcangle_it3.255
p_mcbond_it3.04
p_multtor_nbd0.266
p_xyhbond_nbd0.174
p_singtor_nbd0.172
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor27.5
p_staggered_tor13.7
p_scangle_it6.156
p_scbond_it5.516
p_planar_tor5
p_mcangle_it3.255
p_mcbond_it3.04
p_multtor_nbd0.266
p_xyhbond_nbd0.174
p_singtor_nbd0.172
p_chiral_restr0.127
p_planar_d0.037
p_angle_d0.033
p_plane_restr0.0306
p_bond_d0.016
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms931
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing