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Crystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BFD PDB ENTRY 1BFD
Crystallization Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.704 α = 90 b = 139.938 β = 90 c = 169.054 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH RH-COATED SI MIRROR, RH- COATED TOROIDAL SI MIRROR 2006-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
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 2.2 107.8 97 0.12 8.8 2.9 111569 6 27.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 99.2 0.46 2.2 2.8
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 PDB ENTRY 1BFD 2.2 35 105886 5610 96.5 0.182 0.18 0.1821 0.228 0.2283 RANDOM 21.35
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] 3.37 -1.4 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.652 r_dihedral_angle_4_deg 18.066 r_dihedral_angle_3_deg 13.425 r_dihedral_angle_1_deg 5.852 r_scangle_it 2 r_scbond_it 1.372 r_angle_refined_deg 1.125 r_mcangle_it 1.028 r_mcbond_it 0.914 r_angle_other_deg 0.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.652 r_dihedral_angle_4_deg 18.066 r_dihedral_angle_3_deg 13.425 r_dihedral_angle_1_deg 5.852 r_scangle_it 2 r_scbond_it 1.372 r_angle_refined_deg 1.125 r_mcangle_it 1.028 r_mcbond_it 0.914 r_angle_other_deg 0.858 r_nbd_refined 0.191 r_nbd_other 0.184 r_nbtor_refined 0.168 r_symmetry_vdw_other 0.147 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.128 r_nbtor_other 0.084 r_symmetry_vdw_refined 0.084 r_chiral_restr 0.061 r_bond_refined_d 0.008 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_refined r_metal_ion_other 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 15780 Nucleic Acid Atoms Solvent Atoms 949 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing