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structure of benzoylformate decarboxylases in complex with cofactor TPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BFD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 289.15 0.2M calcium acetate, 0.1M HEPES (pH 7.5) and 40%(w/v) polyethylene glycol (PEG) 400
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.889 α = 90 b = 124.392 β = 122.35 c = 97.758 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 98.15 PIXEL DECTRIS PILATUS3 6M 2017-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 82.59 99.4 0.096 0.104 0.039 7.1 6.8 97121 14.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 98.7 0.726 0.787 0.301 0.826 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1BFD 1.8 82.59 92088 4969 99.22 0.15997 0.15904 0.1591 0.17706 0.1772 RANDOM 20.642
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] 0.04 0.04 -0.28 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.087 r_dihedral_angle_4_deg 13.534 r_dihedral_angle_3_deg 12.051 r_dihedral_angle_1_deg 5.872 r_long_range_B_refined 4.617 r_angle_refined_deg 1.251 r_mcangle_it 0.823 r_scbond_it 0.571 r_mcbond_it 0.455 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.087 r_dihedral_angle_4_deg 13.534 r_dihedral_angle_3_deg 12.051 r_dihedral_angle_1_deg 5.872 r_long_range_B_refined 4.617 r_angle_refined_deg 1.251 r_mcangle_it 0.823 r_scbond_it 0.571 r_mcbond_it 0.455 r_chiral_restr 0.082 r_bond_refined_d 0.008 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_it r_scangle_other 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 7902 Nucleic Acid Atoms Solvent Atoms 1001 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing