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Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diels-Alderase Fab with nM steroid-binding affinity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C1E PDB entry 1C1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 1.5 M ammonium sulfate, 0.15 M sodium citrate, 0.01% PEG 20000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 4.54 72.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.573 α = 90 b = 127.573 β = 90 c = 91.928 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 ADSC QUANTUM 210 2004-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.99996 ALS 8.2.1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.05 50 99.6 0.082 8.2 15.6 4.1 54755 54536 37.9
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) Redundancy Number Unique Reflections (All) 1 2.05 2.29 100 0.525 52.5 2.4 3.9
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 (All) 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 1C1E 2.05 50 51644 51412 2730 99.55 0.17945 0.17945 0.17812 0.1804 0.20399 0.2032 RANDOM 48.637
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] 1.77 0.89 1.77 -2.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.609 r_dihedral_angle_4_deg 17.66 r_dihedral_angle_3_deg 16.154 r_scangle_it 8.307 r_dihedral_angle_1_deg 6.538 r_scbond_it 6.004 r_mcangle_it 3.418 r_mcbond_it 2.215 r_angle_refined_deg 1.674 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.609 r_dihedral_angle_4_deg 17.66 r_dihedral_angle_3_deg 16.154 r_scangle_it 8.307 r_dihedral_angle_1_deg 6.538 r_scbond_it 6.004 r_mcangle_it 3.418 r_mcbond_it 2.215 r_angle_refined_deg 1.674 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.242 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.128 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3349 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement BOS data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing