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Crystal structure of Diels-Alderase CE11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 protein solution (11.7 mg/mL, in 25 mM HEPES, pH 7.5, 150 mM NaCl) was mixed with reservoir solution containing 24.0% w/v PEG 3350 and 0.2 M ammonium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.86 33.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.04 α = 84.12 b = 46.15 β = 83.01 c = 76.91 γ = 66.18
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2012-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 42.2 96 0.0488 14 3.5 47771 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 92.3 0.237 3.94 3.48 6849
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 1E1A 1.8 42.15 45382 2389 96.03 0.1872 0.18485 0.1872 0.23266 0.2348 RANDOM 29.032
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] -1.53 -0.73 -0.32 1.35 1.13 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.787 r_dihedral_angle_4_deg 20.895 r_dihedral_angle_3_deg 14.137 r_dihedral_angle_1_deg 7.311 r_long_range_B_refined 5.301 r_long_range_B_other 5.284 r_scangle_other 3.85 r_mcangle_it 3.315 r_mcangle_other 3.315 r_scbond_it 2.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.787 r_dihedral_angle_4_deg 20.895 r_dihedral_angle_3_deg 14.137 r_dihedral_angle_1_deg 7.311 r_long_range_B_refined 5.301 r_long_range_B_other 5.284 r_scangle_other 3.85 r_mcangle_it 3.315 r_mcangle_other 3.315 r_scbond_it 2.645 r_scbond_other 2.644 r_mcbond_it 2.383 r_mcbond_other 2.382 r_angle_refined_deg 1.71 r_angle_other_deg 0.832 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4713 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction SADABS data scaling