7DCL

Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96I/A38S AB5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QI5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529821% Polyethylene glycol (PEG) 400, bis-tris, ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
2.1141.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.408α = 90
b = 53.408β = 90
c = 251.61γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 11C0.979PAL/PLS11C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.4546.5599.90.1180.120.02188.5534.214826
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.491000.1770.180.0290.99437.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3QI52.4545.53815542099.940.20010.19730.2563RANDOM37.945
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]
-0.25-0.12-0.250.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.208
r_dihedral_angle_3_deg15.92
r_dihedral_angle_1_deg5.001
r_dihedral_angle_4_deg4.641
r_angle_refined_deg1.352
r_angle_other_deg1.215
r_chiral_restr0.055
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.208
r_dihedral_angle_3_deg15.92
r_dihedral_angle_1_deg5.001
r_dihedral_angle_4_deg4.641
r_angle_refined_deg1.352
r_angle_other_deg1.215
r_chiral_restr0.055
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1660
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms95

Software

Software
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction