1M1P

P21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherIdentical protein in P212121 spacegroup

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293ammonium sulphate, bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.69α = 90
b = 34.005β = 110.49
c = 108.313γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42000-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID130.9ESRFID13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.551592.19175884418
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.551.5990

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 REPLACEMENTTHROUGHOUTIdentical protein in P212121 spacegroup1.5514.92917508441844560.174580.17450.172650.21148RANDOM20.014
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]
0.13-0.44-0.12-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg10.398
r_dihedral_angle_1_deg6.08
r_scangle_it3.297
r_scbond_it2.239
r_angle_refined_deg1.573
r_mcangle_it1.567
r_mcbond_it0.889
r_nbd_refined0.357
r_symmetry_vdw_refined0.333
r_symmetry_hbond_refined0.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg10.398
r_dihedral_angle_1_deg6.08
r_scangle_it3.297
r_scbond_it2.239
r_angle_refined_deg1.573
r_mcangle_it1.567
r_mcbond_it0.889
r_nbd_refined0.357
r_symmetry_vdw_refined0.333
r_symmetry_hbond_refined0.174
r_chiral_restr0.108
r_xyhbond_nbd_refined0.108
r_bond_refined_d0.014
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3750
Nucleic Acid Atoms
Solvent Atoms1161
Heterogen Atoms1052

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement