☰ Navigation Tabs
Crystal structure of benzaldehyde lyase in complex with the inhibitor MBP
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 6.9 293 50% PEG 200, 100 mM MES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.90
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.936 α = 90 b = 151.936 β = 90 c = 98.217 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 ADSC QUANTUM 315 2006-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B APS 14-ID-B
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 2.19 46 80.7 0.138 12.4 8 54267 3
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 PDB ENTRY 2AG0 2.49 46 54025 40253 4485 97.21 0.19977 0.19411 0.1933 0.24958 0.2491 RANDOM 50.501
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] 0.7 0.35 0.7 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.956 r_dihedral_angle_3_deg 18.478 r_dihedral_angle_4_deg 16.138 r_dihedral_angle_1_deg 6.848 r_scangle_it 3.612 r_scbond_it 2.398 r_angle_refined_deg 1.916 r_mcangle_it 1.597 r_mcbond_it 0.935 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.956 r_dihedral_angle_3_deg 18.478 r_dihedral_angle_4_deg 16.138 r_dihedral_angle_1_deg 6.848 r_scangle_it 3.612 r_scbond_it 2.398 r_angle_refined_deg 1.916 r_mcangle_it 1.597 r_mcbond_it 0.935 r_nbtor_refined 0.316 r_nbd_refined 0.239 r_metal_ion_refined 0.236 r_symmetry_vdw_refined 0.215 r_symmetry_hbond_refined 0.205 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 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 8158 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing