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The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NXJ PDB ENTRY 1NXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 10% PEG 4000, 0.1 M Na acetate, 10 mM MgCl2, 5 mM pyruvate, 21 mg/ml protein, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.25 62.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.18 α = 90 b = 111.18 β = 90 c = 139.273 γ = 120
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 RAYONIX MX-225 DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR 2009-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97950 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.82 40 90.8 0.099 12 6.7 27093 27093 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.85 89.4 0.273 4.4 2.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NXJ 1.82 28.22 27093 25671 1421 90.84 0.15942 0.15879 0.1662 0.17079 0.1774 RANDOM 40.182
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] -0.84 -0.42 -0.84 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.591 r_dihedral_angle_4_deg 18.391 r_dihedral_angle_3_deg 11.302 r_dihedral_angle_1_deg 6.257 r_scangle_it 1.354 r_angle_refined_deg 1.046 r_scbond_it 0.894 r_angle_other_deg 0.821 r_mcangle_it 0.486 r_mcbond_it 0.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.591 r_dihedral_angle_4_deg 18.391 r_dihedral_angle_3_deg 11.302 r_dihedral_angle_1_deg 6.257 r_scangle_it 1.354 r_angle_refined_deg 1.046 r_scbond_it 0.894 r_angle_other_deg 0.821 r_mcangle_it 0.486 r_mcbond_it 0.412 r_symmetry_vdw_other 0.218 r_nbd_refined 0.201 r_nbd_other 0.186 r_nbtor_refined 0.159 r_symmetry_vdw_refined 0.159 r_symmetry_hbond_refined 0.127 r_xyhbond_nbd_refined 0.09 r_nbtor_other 0.08 r_mcbond_other 0.078 r_chiral_restr 0.059 r_metal_ion_refined 0.014 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1760 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 33
Software Software Software Name Purpose PHASER phasing REFMAC refinement MxDC data collection HKL-2000 data reduction HKL-2000 data scaling