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Computationally Designed Ammelide Deaminase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UZ9 2UZ9.pdb, minus loops and design region
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 10mg/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 coefficient Solvent content 2.67 53.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.827 α = 90 b = 107.315 β = 90 c = 233.62 γ = 90
Symmetry Space Group I 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 mirrors 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.37 117 97.3 0.086 11.8 4.4 44921 43645 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.37 2.45 87 0.339 2.48 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2UZ9.pdb, minus loops and design region 2.37 117.04 44845 41442 2203 97.19 0.20468 0.20241 0.2041 0.24708 RANDOM 41.917
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.235 r_dihedral_angle_3_deg 15.924 r_dihedral_angle_4_deg 13.072 r_dihedral_angle_1_deg 5.512 r_scangle_it 3.172 r_scbond_it 1.963 r_mcangle_it 1.353 r_angle_refined_deg 1.028 r_mcbond_it 0.753 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.235 r_dihedral_angle_3_deg 15.924 r_dihedral_angle_4_deg 13.072 r_dihedral_angle_1_deg 5.512 r_scangle_it 3.172 r_scbond_it 1.963 r_mcangle_it 1.353 r_angle_refined_deg 1.028 r_mcbond_it 0.753 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.176 r_symmetry_hbond_refined 0.159 r_metal_ion_refined 0.078 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 6965 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing