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Crystal structure of trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3 bound to substrate intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.4 M Ammonium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 3.39 63.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.511 α = 90 b = 199.715 β = 92.581 c = 144.511 γ = 90
Symmetry Space Group I 1 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 315r 2010-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0718 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.76 46.7 90.5 0.107 0.994 6.2 2 366454
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.85 90.3 0.61 0.819 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.76 46.7 366310 18623 90.464 0.179 0.1773 0.19 0.2154 0.2253 15.659
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] -0.002 0.136 0.335 -0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.2 r_dihedral_angle_3_deg 12.84 r_dihedral_angle_2_deg 12.211 r_dihedral_angle_1_deg 6.452 r_lrange_it 6.316 r_lrange_other 6.3 r_scangle_it 4.017 r_scangle_other 4.017 r_scbond_it 2.588 r_scbond_other 2.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.2 r_dihedral_angle_3_deg 12.84 r_dihedral_angle_2_deg 12.211 r_dihedral_angle_1_deg 6.452 r_lrange_it 6.316 r_lrange_other 6.3 r_scangle_it 4.017 r_scangle_other 4.017 r_scbond_it 2.588 r_scbond_other 2.588 r_mcangle_other 2.039 r_mcangle_it 2.038 r_angle_refined_deg 1.766 r_mcbond_it 1.347 r_mcbond_other 1.346 r_angle_other_deg 1.068 r_chiral_restr_other 0.953 r_symmetry_nbd_refined 0.341 r_symmetry_xyhbond_nbd_refined 0.318 r_xyhbond_nbd_other 0.283 r_xyhbond_nbd_refined 0.263 r_symmetry_xyhbond_nbd_other 0.248 r_nbd_refined 0.231 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.184 r_nbd_other 0.178 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.084 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20262 Nucleic Acid Atoms Solvent Atoms 3945 Heterogen Atoms 334
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing