3E0L

Computationally Designed Ammelide Deaminase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529810mg/ml HGDA with 0.2mM AD against well solution of 1.8M AS, 0.2M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6753.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.827α = 90
b = 107.315β = 90
c = 233.62γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2008-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.3711797.30.08611.84.4449214364522
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.372.45870.3392.483.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2UZ9.pdb, minus loops and design region2.37117.044484541442220397.190.204680.202410.24708RANDOM41.917
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]
3.1-0.99-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.235
r_dihedral_angle_3_deg15.924
r_dihedral_angle_4_deg13.072
r_dihedral_angle_1_deg5.512
r_scangle_it3.172
r_scbond_it1.963
r_mcangle_it1.353
r_angle_refined_deg1.028
r_mcbond_it0.753
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.235
r_dihedral_angle_3_deg15.924
r_dihedral_angle_4_deg13.072
r_dihedral_angle_1_deg5.512
r_scangle_it3.172
r_scbond_it1.963
r_mcangle_it1.353
r_angle_refined_deg1.028
r_mcbond_it0.753
r_nbtor_refined0.323
r_symmetry_vdw_refined0.221
r_nbd_refined0.217
r_xyhbond_nbd_refined0.176
r_symmetry_hbond_refined0.159
r_metal_ion_refined0.078
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.003
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_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 Atoms6965
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms2

Software

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