☰ Navigation Tabs
Molecular Mechanism of Enantioselective Proton Transfer to Carbon in Catalytic Antibody 14D9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D5I PDB ENTRY 1D5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 45% MPD, 0.1 M TRIS, PH 8.5, 0.2 M AMMONIUM DIHYDROGEN PHOSPHATE,0.1M NAI
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.47 α = 90 b = 97.92 β = 99.28 c = 70.88 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV CONFOCAL MIRRORS 2001-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.79 20 99.4 0.133 0.375 3.7 22991
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 2.79 2.85 85.8 0.42 3.2 3.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1D5I 2.79 20 21887 1011 100 0.207 0.204 0.276 RANDOM 7.94
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] 0.17 -0.74 -1.11 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.021 r_scangle_it 3.414 r_scbond_it 2.11 r_angle_refined_deg 1.259 r_mcangle_it 1.118 r_symmetry_hbond_refined 0.8 r_mcbond_it 0.646 r_symmetry_vdw_refined 0.508 r_nbd_refined 0.285 r_xyhbond_nbd_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.021 r_scangle_it 3.414 r_scbond_it 2.11 r_angle_refined_deg 1.259 r_mcangle_it 1.118 r_symmetry_hbond_refined 0.8 r_mcbond_it 0.646 r_symmetry_vdw_refined 0.508 r_nbd_refined 0.285 r_xyhbond_nbd_refined 0.22 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 6344 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing