3NPU

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 1JCJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52920.2M NaF, 0.1M Bis Tris Propane, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.2846.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.222α = 90
b = 53.295β = 110.19
c = 81.846γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirros2008-06-22MSINGLE 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
12.255097.80.0810.07722.286.5235995119330.25
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)
12.252.3383.80.2170.1954.84.92034

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 REPLACEMENTTHROUGHOUT1JCJ2.255022380120797.280.191980.189270.24116RANDOM30.257
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]
0.81-1.220.14-1.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.272
r_dihedral_angle_4_deg17.007
r_dihedral_angle_3_deg15.891
r_dihedral_angle_1_deg7.94
r_scangle_it4.105
r_scbond_it2.672
r_angle_refined_deg1.733
r_mcangle_it1.515
r_mcbond_it0.944
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.272
r_dihedral_angle_4_deg17.007
r_dihedral_angle_3_deg15.891
r_dihedral_angle_1_deg7.94
r_scangle_it4.105
r_scbond_it2.672
r_angle_refined_deg1.733
r_mcangle_it1.515
r_mcbond_it0.944
r_nbtor_refined0.293
r_symmetry_vdw_refined0.218
r_nbd_refined0.199
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.131
r_chiral_restr0.122
r_bond_refined_d0.02
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3651
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms

Software

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