3NQV

Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R5 7/4A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH4.62770.2M (NH4)2SO4, 0.1M NaAC-3H2O, 30% PEG MME 2000, pH 4.6, Microbatch, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.448.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.524α = 90
b = 64.725β = 104.69
c = 49.032γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Mirrors2009-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.75095.80.1310.11314.55.2301272886226.17
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)
11.71.7392.40.370.3782.63.51358

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 REPLACEMENTTHROUGHOUT3NPU1.75027408145195.760.206380.204840.23364RANDOM26.171
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]
-0.481.01-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.561
r_dihedral_angle_4_deg12.211
r_dihedral_angle_3_deg11.809
r_dihedral_angle_1_deg10.73
r_sphericity_free7.048
r_rigid_bond_restr5.425
r_scbond_it5.394
r_scangle_it4.86
r_sphericity_bonded4.571
r_mcangle_it1.656
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.561
r_dihedral_angle_4_deg12.211
r_dihedral_angle_3_deg11.809
r_dihedral_angle_1_deg10.73
r_sphericity_free7.048
r_rigid_bond_restr5.425
r_scbond_it5.394
r_scangle_it4.86
r_sphericity_bonded4.571
r_mcangle_it1.656
r_angle_refined_deg1.436
r_mcbond_it1.039
r_chiral_restr0.122
r_bond_refined_d0.012
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 Atoms1822
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms9

Software

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