3NPW

In silico designed of an improved Kemp eliminase KE70 mutant 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 DROP62920.2M NH4Cl, MES, 20% PEG 6000 , VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.4850.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.386α = 90
b = 82.872β = 90
c = 127.964γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2010-06-24MSINGLE 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
12.145099.90.0810.05624.27313843135328.9
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)
12.152.2398.90.3940.3092.95.53047

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 REPLACEMENTTHROUGHOUT3NPU2.145029719157499.590.221640.219630.25874RANDOM28.924
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]
0.92-21.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.557
r_dihedral_angle_3_deg15.479
r_dihedral_angle_4_deg14.076
r_dihedral_angle_1_deg7.09
r_scangle_it4.092
r_scbond_it2.666
r_angle_refined_deg1.636
r_mcangle_it1.53
r_mcbond_it0.982
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.557
r_dihedral_angle_3_deg15.479
r_dihedral_angle_4_deg14.076
r_dihedral_angle_1_deg7.09
r_scangle_it4.092
r_scbond_it2.666
r_angle_refined_deg1.636
r_mcangle_it1.53
r_mcbond_it0.982
r_nbtor_refined0.295
r_symmetry_vdw_refined0.245
r_nbd_refined0.205
r_symmetry_hbond_refined0.148
r_xyhbond_nbd_refined0.129
r_chiral_restr0.105
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 Atoms3608
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms

Software

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