☰ Navigation Tabs
Structure of benzaldehyde lyase A28S mutant with benzoylphosphonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 298 100 mM MES, 50% v/v PEG 200, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.856 α = 90 b = 150.856 β = 90 c = 97.24 γ = 120
Symmetry Space Group P 32 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 100 CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2006-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
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 2.25 50 99.3 0.097 10.2 8.6 60682 60258 2 2
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) 2.25 2.33 94.8 0.684 1.53 4.5
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 3D7K 2.3 45.55 60682 50883 5711 99.58 0.20728 0.20431 0.2028 0.23357 0.2319 RANDOM 48.093
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] 0.25 0.13 0.25 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.477 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_4_deg 12.3 r_dihedral_angle_1_deg 4.367 r_angle_refined_deg 1.289 r_scangle_it 1.241 r_mcangle_it 1.186 r_scbond_it 0.706 r_mcbond_it 0.658 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.477 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_4_deg 12.3 r_dihedral_angle_1_deg 4.367 r_angle_refined_deg 1.289 r_scangle_it 1.241 r_mcangle_it 1.186 r_scbond_it 0.706 r_mcbond_it 0.658 r_nbtor_refined 0.292 r_chiral_restr 0.269 r_symmetry_vdw_refined 0.171 r_nbd_refined 0.168 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.101 r_metal_ion_refined 0.095 r_bond_refined_d 0.008 r_gen_planes_refined 0.002 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8160 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 80
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection locally data collection HKL-2000 data reduction MOLREP phasing