3NPX

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 DROP5.52920.1M NaCl, 20% PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.5150.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.135α = 90
b = 83.331β = 90
c = 129.203γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.975ESRFID14-4

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
11.795099.60.0910.09528.79.5534575324319.03
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)
11.81.8699.10.310.295.98.45234

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 REPLACEMENTTHROUGHOUT3NPU1.795050467270399.180.19830.196970.22313RANDOM19.029
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]
0.25-1.150.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.214
r_dihedral_angle_4_deg12.76
r_dihedral_angle_3_deg11.691
r_dihedral_angle_1_deg7.008
r_scangle_it3.579
r_scbond_it2.194
r_angle_refined_deg1.258
r_mcangle_it1.16
r_mcbond_it0.712
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.214
r_dihedral_angle_4_deg12.76
r_dihedral_angle_3_deg11.691
r_dihedral_angle_1_deg7.008
r_scangle_it3.579
r_scbond_it2.194
r_angle_refined_deg1.258
r_mcangle_it1.16
r_mcbond_it0.712
r_nbtor_refined0.298
r_nbd_refined0.198
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.123
r_symmetry_hbond_refined0.094
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3698
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms

Software

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