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Crystal Structure of a Novel Engineered Retroaldolase: RA-61
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M4W TRUNCATED 1m4w
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 1.9M Ammonium Sulfate, 0.1M MES pH 6.5, 5% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K 2 VAPOR DIFFUSION, HANGING DROP 6.5 298 2.0M Ammonium Sulfate, 0.1M MES pH 6.5, 5% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K 3 VAPOR DIFFUSION, HANGING DROP 6.5 298 2.1M Ammonium Sulfate, 0.1M MES pH 6.5, 5% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.19 α = 90 b = 66.06 β = 90 c = 66.07 γ = 90
Symmetry Space Group P 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 IMAGE PLATE RIGAKU RAXIS IV Mirrors 2007-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 46.73 97.5 0.059 12 3.49 16489 16082 29.9
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 1.86 83.3 0.22 3.1 2.45 1347
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT TRUNCATED 1m4w 1.8 33.71 16082 16082 819 97.53 0.206 0.203 0.248 0.2469 RANDOM 17.723
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] 0.73 -0.12 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.423 r_dihedral_angle_4_deg 11.772 r_dihedral_angle_3_deg 10.634 r_dihedral_angle_1_deg 7.317 r_scangle_it 1.136 r_angle_refined_deg 1.069 r_scbond_it 0.835 r_mcangle_it 0.539 r_mcbond_it 0.313 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.423 r_dihedral_angle_4_deg 11.772 r_dihedral_angle_3_deg 10.634 r_dihedral_angle_1_deg 7.317 r_scangle_it 1.136 r_angle_refined_deg 1.069 r_scbond_it 0.835 r_mcangle_it 0.539 r_mcbond_it 0.313 r_nbtor_refined 0.301 r_nbd_refined 0.171 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.1 r_symmetry_hbond_refined 0.079 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1532 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 12
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction