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Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A53 PDB ENTRY 1A53, MODIFIED TO PREVENT MODEL BIAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 298 Protein at 5mg/ml in 100mm NaCl, 25mm TRIS pH7.5. Crystals grew at and near 2M ammonium sulfate, 4% PEG400, 100mN Na acetate pH5.5, vapor diffusion, temperature 298k, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.45 49.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.684 α = 90 b = 62.684 β = 90 c = 123.68 γ = 120
Symmetry Space Group P 31 2 1
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 RIGAKU SATURN 944+ VARIMAX HF 2009-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.091 50 99 0.037 22 2.9 17137 2 29.82
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) 1 2.091 2.16 95.2 0.153 6.86 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1A53, MODIFIED TO PREVENT MODEL BIAS 2.091 19.47 16229 868 99.3 0.227 0.227 0.2124 0.258 0.2634 RANDOM 32.85
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.439 r_dihedral_angle_4_deg 16.778 r_dihedral_angle_3_deg 15.268 r_dihedral_angle_1_deg 4.933 r_scangle_it 3.215 r_scbond_it 1.908 r_mcangle_it 1.376 r_angle_refined_deg 1.028 r_mcbond_it 0.765 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.439 r_dihedral_angle_4_deg 16.778 r_dihedral_angle_3_deg 15.268 r_dihedral_angle_1_deg 4.933 r_scangle_it 3.215 r_scbond_it 1.908 r_mcangle_it 1.376 r_angle_refined_deg 1.028 r_mcbond_it 0.765 r_nbtor_refined 0.299 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.066 r_bond_refined_d 0.008 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_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 Atoms Number Protein Atoms 1995 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 27
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling