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Structure of benzaldehyde lyase A28S mutant with monomethyl benzoylphosphonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 298 100 mM MES (pH 6.9), 50% v/v PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.962 α = 90 b = 150.962 β = 90 c = 195.56 γ = 120
Symmetry Space Group P 31 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 2.7 50 97.5 0.122 7.9 10.1 70834 69063 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) 2.7 2.8 79.4 0.731 1.33 5.2
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 2AG0 2.8 47.89 70834 57155 6394 99.44 0.21744 0.21258 0.2115 0.26038 0.2595 RANDOM 76.129
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] 0.16 0.08 0.16 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.348 r_dihedral_angle_3_deg 17.296 r_dihedral_angle_4_deg 15.76 r_dihedral_angle_1_deg 5.254 r_mcangle_it 2.338 r_scangle_it 1.782 r_mcbond_it 1.289 r_angle_refined_deg 1.097 r_scbond_it 0.988 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.348 r_dihedral_angle_3_deg 17.296 r_dihedral_angle_4_deg 15.76 r_dihedral_angle_1_deg 5.254 r_mcangle_it 2.338 r_scangle_it 1.782 r_mcbond_it 1.289 r_angle_refined_deg 1.097 r_scbond_it 0.988 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.071 r_symmetry_hbond_refined 0.071 r_metal_ion_refined 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 16336 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 108
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection locally data collection