3HNJ

Crystal structure of the Zn-induced tetramer of the engineered cyt cb562 variant RIDC-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QLA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293100 mM BIS-TRIS, 25% PEG 3350, 3.4 mM zinc chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.448α = 90
b = 65.316β = 104.7
c = 70.773γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.976SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
1230.792.50.0440.04411.0222.628830
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1192.40.1760.1762.72.5

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2QLA230.72883024925193092.560.227880.224450.27159RANDOM26.016
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]
0.030.030.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.374
r_dihedral_angle_3_deg18.618
r_dihedral_angle_4_deg6.816
r_dihedral_angle_1_deg4.514
r_scangle_it1.718
r_angle_refined_deg1.185
r_scbond_it1.142
r_mcangle_it0.692
r_mcbond_it0.371
r_nbtor_refined0.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.374
r_dihedral_angle_3_deg18.618
r_dihedral_angle_4_deg6.816
r_dihedral_angle_1_deg4.514
r_scangle_it1.718
r_angle_refined_deg1.185
r_scbond_it1.142
r_mcangle_it0.692
r_mcbond_it0.371
r_nbtor_refined0.279
r_symmetry_vdw_refined0.256
r_nbd_refined0.204
r_xyhbond_nbd_refined0.174
r_symmetry_hbond_refined0.167
r_metal_ion_refined0.091
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3268
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms180

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOLREPphasing