4EID

Crystal structure of cytochrome c6 Q57V mutant from Synechococcus sp. PCC 7002


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
2.0239.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.781α = 90
b = 27.637β = 101.16
c = 44.099γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANELmirrors2010-07-13MSINGLE 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
11.135099.10.0515.33.32814428144-313.3
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)
11.131.296.80.45121.74430

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3DR01.1343.2627159271599861000.139310.139310.137970.17574RANDOM7.156
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]
0.180.850.080.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.816
r_dihedral_angle_4_deg20.177
r_dihedral_angle_3_deg10.14
r_dihedral_angle_1_deg5.598
r_scangle_it4.272
r_scbond_it3.356
r_mcangle_it2.364
r_angle_refined_deg1.872
r_mcbond_it1.8
r_rigid_bond_restr1.528
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.816
r_dihedral_angle_4_deg20.177
r_dihedral_angle_3_deg10.14
r_dihedral_angle_1_deg5.598
r_scangle_it4.272
r_scbond_it3.356
r_mcangle_it2.364
r_angle_refined_deg1.872
r_mcbond_it1.8
r_rigid_bond_restr1.528
r_angle_other_deg1.244
r_mcbond_other0.872
r_chiral_restr0.127
r_bond_refined_d0.023
r_gen_planes_refined0.016
r_gen_planes_other0.009
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms660
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms55

Software

Software
Software NamePurpose
AUTOMARdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling