5BRU

Catalytic Improvement of an Artificial Metalloenzyme by Computational Design


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZP9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.92982.6 M ammonium sulfate, 50 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.1141.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.308α = 90
b = 41.689β = 104.26
c = 72.343γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.30510SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.670.1190.30.0960.0480.99611.64.729218
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6355.40.7190.4010.4822.13.8877

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 REPLACEMENTTHROUGHOUT3ZP91.670.1127665154289.790.140080.137170.19358RANDOM18.147
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]
0.020.57-0.570.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.022
r_dihedral_angle_4_deg24.221
r_sphericity_free18.156
r_dihedral_angle_3_deg13.03
r_dihedral_angle_1_deg7.109
r_sphericity_bonded6.809
r_long_range_B_refined3.748
r_long_range_B_other3.089
r_rigid_bond_restr3.012
r_scbond_it2.988
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.022
r_dihedral_angle_4_deg24.221
r_sphericity_free18.156
r_dihedral_angle_3_deg13.03
r_dihedral_angle_1_deg7.109
r_sphericity_bonded6.809
r_long_range_B_refined3.748
r_long_range_B_other3.089
r_rigid_bond_restr3.012
r_scbond_it2.988
r_scangle_other2.796
r_scbond_other2.562
r_mcangle_it2.233
r_mcangle_other2.232
r_mcbond_it2.092
r_mcbond_other2.035
r_angle_refined_deg1.838
r_angle_other_deg1.004
r_chiral_restr0.115
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.003
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 Atoms2059
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction