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Crystal structure of the anaerobic DesB-Protocatechuate (PCA) complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WR8 DesB substrate-free form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.75 277 25% PEG8000, 0.1M SODIUM ACETATE, 0.1M HEPES-NAOH, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.83 α = 90 b = 61.014 β = 97.84 c = 117.545 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2010-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.4 54.1 97.7 0.041 20.63 3.86 32061 31324
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 93 4.33 3.51
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 (All) 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 DesB substrate-free form 2.4 54.04 29789 29789 1568 100 0.22 0.22 0.217 0.276 0.269 RANDOM 65.11
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] -1.68 1.78 1.89 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.301 r_dihedral_angle_3_deg 18.199 r_dihedral_angle_4_deg 16.446 r_dihedral_angle_1_deg 6.016 r_scangle_it 2.33 r_scbond_it 1.5 r_angle_refined_deg 1.189 r_mcangle_it 0.857 r_mcbond_it 0.467 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.301 r_dihedral_angle_3_deg 18.199 r_dihedral_angle_4_deg 16.446 r_dihedral_angle_1_deg 6.016 r_scangle_it 2.33 r_scbond_it 1.5 r_angle_refined_deg 1.189 r_mcangle_it 0.857 r_mcbond_it 0.467 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6378 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 13
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling