5K68

Designed Artificial Cupredoxins


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42742.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4
Crystal Properties
Matthews coefficientSolvent content
2.346.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.69α = 90
b = 57.69β = 90
c = 183.61γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.00000ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.445.999.80.069112.76.831080
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)
11.41.4298.81.4466.6

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 REPLACEMENTTHROUGHOUT2qcb1.445.929542148999.660.143510.141620.18129RANDOM20.519
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]
-0.19-0.190.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.582
r_sphericity_free25.982
r_dihedral_angle_4_deg15.845
r_sphericity_bonded14.704
r_dihedral_angle_3_deg13.14
r_long_range_B_refined7.515
r_dihedral_angle_1_deg7.412
r_scbond_it6.608
r_rigid_bond_restr6.026
r_long_range_B_other5.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.582
r_sphericity_free25.982
r_dihedral_angle_4_deg15.845
r_sphericity_bonded14.704
r_dihedral_angle_3_deg13.14
r_long_range_B_refined7.515
r_dihedral_angle_1_deg7.412
r_scbond_it6.608
r_rigid_bond_restr6.026
r_long_range_B_other5.57
r_scangle_other5.13
r_scbond_other4.966
r_angle_refined_deg3.915
r_mcangle_other3.773
r_mcangle_it3.761
r_mcbond_it3.034
r_mcbond_other2.894
r_angle_other_deg1.984
r_chiral_restr0.193
r_bond_refined_d0.032
r_gen_planes_refined0.013
r_bond_other_d0.003
r_gen_planes_other0.003
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms924
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing