5BRW

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
2.0640.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.914α = 90
b = 41.297β = 104.38
c = 72.127γ = 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
11.469.87960.080.0370.99912.45.545248
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)
11.41.4293.81.6160.7650.38415.22171

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 REPLACEMENTTHROUGHOUT3zp91.469.8742998222495.570.14150.13880.1936RANDOM21.966
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]
0.52-0.160.39-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.878
r_sphericity_free27.077
r_dihedral_angle_4_deg20.515
r_sphericity_bonded15.666
r_dihedral_angle_3_deg13.39
r_dihedral_angle_1_deg6.769
r_rigid_bond_restr3.917
r_mcangle_it3.009
r_mcbond_it2.456
r_mcbond_other2.418
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.878
r_sphericity_free27.077
r_dihedral_angle_4_deg20.515
r_sphericity_bonded15.666
r_dihedral_angle_3_deg13.39
r_dihedral_angle_1_deg6.769
r_rigid_bond_restr3.917
r_mcangle_it3.009
r_mcbond_it2.456
r_mcbond_other2.418
r_angle_refined_deg1.835
r_angle_other_deg1.046
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms19

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction