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Crystal structure of trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3
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 3.38 63.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.7 α = 90 b = 199.89 β = 133.79 c = 144.15 γ = 90
Symmetry Space Group C 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 4 2010-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
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 1.96 36.04 95.6 0.134 0.933 5.1 2 277447
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 1.96 2.06 0.218 0.897 3.4
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 1.96 36.04 277097 13909 94.739 0.141 0.1394 0.1515 0.1684 0.1706 15.55
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] 3.704 -0.56 4.342 -8.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.549 r_dihedral_angle_2_deg 13.42 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_1_deg 6.388 r_lrange_it 6.217 r_lrange_other 5.898 r_scangle_it 4.182 r_scangle_other 4.138 r_mcangle_it 2.921 r_mcangle_other 2.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.549 r_dihedral_angle_2_deg 13.42 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_1_deg 6.388 r_lrange_it 6.217 r_lrange_other 5.898 r_scangle_it 4.182 r_scangle_other 4.138 r_mcangle_it 2.921 r_mcangle_other 2.921 r_scbond_it 2.839 r_scbond_other 2.807 r_mcbond_it 2.072 r_mcbond_other 2.065 r_angle_refined_deg 1.815 r_angle_other_deg 0.983 r_symmetry_nbd_refined 0.383 r_symmetry_xyhbond_nbd_refined 0.292 r_xyhbond_nbd_refined 0.254 r_nbd_other 0.239 r_nbd_refined 0.235 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_other 0.151 r_xyhbond_nbd_other 0.133 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_24 0.067 r_ncsr_local_group_17 0.066 r_ncsr_local_group_5 0.063 r_ncsr_local_group_6 0.063 r_ncsr_local_group_7 0.063 r_ncsr_local_group_8 0.063 r_ncsr_local_group_12 0.063 r_ncsr_local_group_18 0.063 r_ncsr_local_group_1 0.062 r_ncsr_local_group_14 0.062 r_ncsr_local_group_16 0.062 r_ncsr_local_group_21 0.062 r_ncsr_local_group_22 0.062 r_ncsr_local_group_15 0.061 r_ncsr_local_group_25 0.061 r_ncsr_local_group_3 0.06 r_ncsr_local_group_11 0.06 r_ncsr_local_group_13 0.06 r_ncsr_local_group_23 0.059 r_ncsr_local_group_28 0.059 r_ncsr_local_group_9 0.057 r_ncsr_local_group_4 0.056 r_ncsr_local_group_10 0.056 r_ncsr_local_group_19 0.056 r_ncsr_local_group_26 0.056 r_ncsr_local_group_2 0.055 r_ncsr_local_group_20 0.054 r_ncsr_local_group_27 0.054 r_gen_planes_other 0.014 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20265 Nucleic Acid Atoms Solvent Atoms 3180 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing