3NQ2

Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R2 3/5G


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.5277PCB pH5.0, PEG 1500, pH 5.5, Microbatch, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4549.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.008α = 90
b = 96.228β = 125.88
c = 71.274γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV++mirror2008-08-05MSINGLE 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
12.025097.90.070.05119.65.1356833493419.24
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)
12.022.0995.30.320.2823.074.43420

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 REPLACEMENTTHROUGHOUT3NPU2.025033171175797.850.208060.205210.26019RANDOM19.241
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]
-0.39-0.4-0.280.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.822
r_dihedral_angle_4_deg14.889
r_dihedral_angle_3_deg13.968
r_dihedral_angle_1_deg6.211
r_scangle_it3.648
r_scbond_it2.326
r_angle_refined_deg1.338
r_mcangle_it1.304
r_mcbond_it0.856
r_angle_other_deg0.618
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.822
r_dihedral_angle_4_deg14.889
r_dihedral_angle_3_deg13.968
r_dihedral_angle_1_deg6.211
r_scangle_it3.648
r_scbond_it2.326
r_angle_refined_deg1.338
r_mcangle_it1.304
r_mcbond_it0.856
r_angle_other_deg0.618
r_nbd_other0.505
r_nbtor_refined0.293
r_symmetry_vdw_refined0.239
r_nbd_refined0.204
r_xyhbond_nbd_refined0.134
r_chiral_restr0.093
r_symmetry_hbond_refined0.065
r_bond_refined_d0.016
r_bond_other_d0.014
r_gen_planes_refined0.005
r_gen_planes_other0.002
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 Atoms3640
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms10

Software

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