5WBD

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - N49A


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, 2.0 M sodium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.1943.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.51α = 90
b = 57.51β = 90
c = 174.81γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21ALS8.2.2

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
11.554.6399.918.611.224051
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5

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 2QCB1.554.6322773123599.750.154950.153740.17782RANDOM15.492
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]
-0.13-0.130.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.725
r_sphericity_free17.45
r_dihedral_angle_4_deg14.886
r_dihedral_angle_3_deg12.381
r_dihedral_angle_1_deg6.356
r_sphericity_bonded3.112
r_long_range_B_refined1.655
r_long_range_B_other1.476
r_angle_refined_deg1.399
r_angle_other_deg1.266
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.725
r_sphericity_free17.45
r_dihedral_angle_4_deg14.886
r_dihedral_angle_3_deg12.381
r_dihedral_angle_1_deg6.356
r_sphericity_bonded3.112
r_long_range_B_refined1.655
r_long_range_B_other1.476
r_angle_refined_deg1.399
r_angle_other_deg1.266
r_mcangle_other1.113
r_mcangle_it1.099
r_rigid_bond_restr1.069
r_scangle_other1.017
r_scbond_it0.97
r_scbond_other0.97
r_mcbond_it0.867
r_mcbond_other0.828
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms933
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing