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1.65 Angstrom structure of Benzaldehyde Lyase complexed with 2-methyl- 2,4-pentanediol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AG0 PDB ENTRY 2AG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M TRIS/HCL, PH 7.5, 0.2 M POTASSIUM ISOTHIOCYANATE, 10% (W/V) POLYETHYLENE GLYCOL 1000 MW, 10% POLYETHYLENE GLYCOL 8000 MW, AND 2-METHYLPENTANE-2-4-DIOL 45% (V/V); PROTEIN CONCENTRATION 5 MG ML-1 WITH A THREEFOLD STOICHIOMETRIC EXCESS OF THIAMINE DIPHOSPHATE (THDP).
Crystal Properties Matthews coefficient Solvent content 1 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.462 α = 90 b = 121.601 β = 90 c = 162.957 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 ADSC CCD 2005-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.65 50 99 0.13 5.5 5.1 249612
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 1.65 1.68 100 0.88 1.5 5
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 2AG0 1.65 97.59 236875 12534 99.7 0.168 0.167 0.1667 0.192 0.1913 RANDOM 12.59
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] -0.32 0.75 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.238 r_dihedral_angle_4_deg 18.7 r_dihedral_angle_3_deg 12.38 r_dihedral_angle_1_deg 5.608 r_scangle_it 2.877 r_scbond_it 1.835 r_angle_refined_deg 1.27 r_mcangle_it 0.967 r_mcbond_it 0.561 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.238 r_dihedral_angle_4_deg 18.7 r_dihedral_angle_3_deg 12.38 r_dihedral_angle_1_deg 5.608 r_scangle_it 2.877 r_scbond_it 1.835 r_angle_refined_deg 1.27 r_mcangle_it 0.967 r_mcbond_it 0.561 r_nbtor_refined 0.303 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 16184 Nucleic Acid Atoms Solvent Atoms 1881 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing