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Crystal structure of 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe, an engineered Diels-Alderase Fab with modified specificity and catalytic activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.75M ammoniumsulfate, 0.15M sodiumcitrate, 0.01% PEG20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.55 72.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.73 α = 90 b = 128.73 β = 90 c = 92.342 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 2005-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
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 2.3 50 99.4 0.057 20.5 4.3 39314
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 2.3 2.38 99.7 0.557 2.4
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 2O5X 2.3 50 37304 1973 99.4 0.19362 0.19225 0.1952 0.2192 0.2219 RANDOM 52.729
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] 2.03 1.01 2.03 -3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 15.367 r_dihedral_angle_1_deg 7.086 r_scangle_it 2.949 r_scbond_it 2.251 r_angle_refined_deg 1.816 r_mcangle_it 1.359 r_mcbond_it 1.055 r_angle_other_deg 0.969
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 18.831 r_dihedral_angle_3_deg 15.367 r_dihedral_angle_1_deg 7.086 r_scangle_it 2.949 r_scbond_it 2.251 r_angle_refined_deg 1.816 r_mcangle_it 1.359 r_mcbond_it 1.055 r_angle_other_deg 0.969 r_symmetry_vdw_other 0.271 r_symmetry_hbond_refined 0.219 r_symmetry_vdw_refined 0.217 r_nbd_other 0.2 r_mcbond_other 0.2 r_nbd_refined 0.191 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.103 r_nbtor_other 0.087 r_xyhbond_nbd_other 0.069 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3344 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 184
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling