1H29

Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Structure of the 16-heme Cytochrome c HmcA at 2.5 A resolution and a view of its role in transmembrane electron transfer


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5277EACH CRYSTALLIZATION ASSAY WAS PREPARED BY ADDING 5 UL OF THE PROTEIN SOLUTION (10 MG/ML) TO A DIALYSIS BUTTON WHICH WAS THEN COMPLETELY SOAKED IN THE CRYSTALLIZATION WAS THEN COMPLETELY SOAKED IN THE SOLUTION. AFTER A FEW DAYS AT 4C, SMALL HEXAGONAL BIPYRAMIDS STARTED STARTED TO APPEAR AND REACHED THEIR MAXIMUM SIZE AFTER ONE WEEK. THE BEST CRYOCRYSTALLOGRAPHY CONDITIONS WERE OBTAINED BY SOAKING THESE CRYSTALS IN A CRYSTALLIZATION SOLUTION CONTAINING 7.5% MPD, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.855

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 220.39α = 90
b = 220.39β = 90
c = 102.64γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4rMIRRORS2001-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.52591.30.06411.96.589606
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)
12.52.59840.3543

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.513085075449492.10.1950.1920.258RANDOM30.61
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]
1.570.791.57-2.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.751
r_scangle_it2.385
r_scbond_it1.647
r_angle_refined_deg1.547
r_mcangle_it0.97
r_mcbond_it0.515
r_nbd_refined0.222
r_symmetry_hbond_refined0.214
r_symmetry_vdw_refined0.2
r_xyhbond_nbd_refined0.152
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15038
Nucleic Acid Atoms
Solvent Atoms497
Heterogen Atoms2752

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling