5BRV

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
2.0941.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.23α = 90
b = 41.544β = 104.11
c = 72.13γ = 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
11.669.9685.60.1050.0520.9979.5527511
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)
11.61.63451.0780.5540.4311.34.5704

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 REPLACEMENTTHROUGHOUT3ZP91.669.9626057144185.20.18710.18460.2296RANDOM23.532
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]
0.210.75-0.930.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.952
r_dihedral_angle_4_deg21.906
r_dihedral_angle_3_deg14.643
r_dihedral_angle_1_deg11.753
r_mcangle_it3.079
r_mcbond_it2.087
r_mcbond_other2.052
r_angle_refined_deg1.879
r_angle_other_deg1.023
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.952
r_dihedral_angle_4_deg21.906
r_dihedral_angle_3_deg14.643
r_dihedral_angle_1_deg11.753
r_mcangle_it3.079
r_mcbond_it2.087
r_mcbond_other2.052
r_angle_refined_deg1.879
r_angle_other_deg1.023
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2059
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction