3NPV

Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52920.2M NaNitrat, 0.1M Bis Tris-propane, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.346.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.595α = 90
b = 53.518β = 110.34
c = 81.702γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002010-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.485099.60.1010.09615.54.1844888415117.6
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)
11.481.5198.90.3540.3152.63.84147

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 REPLACEMENTTHROUGHOUT3NPU1.485078893415098.770.14470.143310.17017RANDOM17.632
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]
-0.36-0.470.42-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.827
r_dihedral_angle_4_deg16.494
r_dihedral_angle_3_deg12.039
r_scangle_it9.449
r_scbond_it6.303
r_dihedral_angle_1_deg6.027
r_mcangle_it3.923
r_rigid_bond_restr3.011
r_mcbond_it2.726
r_angle_refined_deg2.021
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.827
r_dihedral_angle_4_deg16.494
r_dihedral_angle_3_deg12.039
r_scangle_it9.449
r_scbond_it6.303
r_dihedral_angle_1_deg6.027
r_mcangle_it3.923
r_rigid_bond_restr3.011
r_mcbond_it2.726
r_angle_refined_deg2.021
r_chiral_restr0.322
r_bond_refined_d0.025
r_gen_planes_refined0.013
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3683
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms

Software

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