5WBA

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - WT


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42980.1 M sodium acetate, pH 4.0, 2.6 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.2846.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.51α = 90
b = 57.51β = 90
c = 183.13γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.554.8795.820.2724121
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.53

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 REPLACEMENTTHROUGHOUTPDB entry 2QCB1.554.8722891119995.540.140890.140340.15135RANDOM19.598
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]
-0.02-0.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.208
r_sphericity_free21.632
r_dihedral_angle_4_deg12.988
r_dihedral_angle_3_deg11.321
r_dihedral_angle_1_deg6.672
r_sphericity_bonded5.023
r_long_range_B_other2.465
r_long_range_B_refined2.447
r_mcangle_other1.626
r_mcangle_it1.547
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.208
r_sphericity_free21.632
r_dihedral_angle_4_deg12.988
r_dihedral_angle_3_deg11.321
r_dihedral_angle_1_deg6.672
r_sphericity_bonded5.023
r_long_range_B_other2.465
r_long_range_B_refined2.447
r_mcangle_other1.626
r_mcangle_it1.547
r_scangle_other1.494
r_angle_refined_deg1.433
r_scbond_it1.234
r_scbond_other1.233
r_mcbond_it1.227
r_mcbond_other0.997
r_rigid_bond_restr0.986
r_angle_other_deg0.886
r_chiral_restr0.088
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms936
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing