6LDG

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IQ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529825% PEG 3350, 100 mM HEPES pH 7.5, 200 mM sodium chloride
Crystal Properties
Matthews coefficientSolvent content
2.2144.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.723α = 90
b = 53.723β = 90
c = 250.757γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702019-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.987PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9828.3899.80.129105.84015931
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.011000.32340.2

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 REPLACEMENTTHROUGHOUT3IQ61.9828.381472276999.790.17060.16790.2213RANDOM22.766
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]
0.150.080.15-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg47.476
r_dihedral_angle_3_deg15.292
r_dihedral_angle_4_deg5.691
r_dihedral_angle_1_deg5.32
r_angle_refined_deg1.709
r_angle_other_deg1.465
r_chiral_restr0.081
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg47.476
r_dihedral_angle_3_deg15.292
r_dihedral_angle_4_deg5.691
r_dihedral_angle_1_deg5.32
r_angle_refined_deg1.709
r_angle_other_deg1.465
r_chiral_restr0.081
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1658
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms97

Software

Software
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction