3NQ8

Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R4 8/5A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JCJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.32920.1M Ammonium Nitrat, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
1.8834.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.756α = 90
b = 52.756β = 90
c = 153.694γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCD2008-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.939ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.45097.90.0580.05357.2820.5439504302714.63
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.421000.2430.21113.623.12163

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 REPLACEMENTTHROUGHOUT1JCJ1.449.8840785215597.880.174920.174080.1903RANDOM14.627
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]
0.250.25-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.174
r_dihedral_angle_4_deg14.869
r_dihedral_angle_3_deg10.883
r_dihedral_angle_1_deg5.928
r_sphericity_free3.946
r_scangle_it3.176
r_sphericity_bonded2.384
r_scbond_it2.123
r_mcangle_it1.354
r_rigid_bond_restr1.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.174
r_dihedral_angle_4_deg14.869
r_dihedral_angle_3_deg10.883
r_dihedral_angle_1_deg5.928
r_sphericity_free3.946
r_scangle_it3.176
r_sphericity_bonded2.384
r_scbond_it2.123
r_mcangle_it1.354
r_rigid_bond_restr1.244
r_angle_refined_deg1.133
r_mcbond_it0.824
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1801
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms17

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling