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Complex of [E160A-E189A] trichosanthin and adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QD2 PDB Entry 1QD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 Tris-HCl, PEG4000, magnesium chloride, adenine hemisulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.07 40.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.928 α = 90 b = 75.299 β = 90 c = 78.65 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 IMAGE PLATE MARRESEARCH Mirrors 2001-10-03 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) R Sym 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 1.93 54.391 99.3 0.056 0.056 9.2 3.7 16683 2 2 12.008
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.93 2.03 99.3 0.155 0.132 5.4 3.6 2290
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1QD2 1.93 54.23 2 2 20467 16473 878 99.3 0.16011 0.16011 0.15758 0.1722 0.20771 0.2232 RANDOM 10.951
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] -1.3 0.73 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.055 r_scangle_it 4.874 r_scbond_it 3.07 r_mcangle_it 1.838 r_angle_refined_deg 1.775 r_mcbond_it 1.063 r_angle_other_deg 0.926 r_symmetry_vdw_other 0.306 r_symmetry_vdw_refined 0.258 r_nbd_other 0.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.055 r_scangle_it 4.874 r_scbond_it 3.07 r_mcangle_it 1.838 r_angle_refined_deg 1.775 r_mcbond_it 1.063 r_angle_other_deg 0.926 r_symmetry_vdw_other 0.306 r_symmetry_vdw_refined 0.258 r_nbd_other 0.254 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.111 r_nbtor_other 0.091 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_xyhbond_nbd_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1913 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 10
Software Software Software Name Purpose MOSFLM data reduction TRUNCATE data reduction AMoRE phasing REFMAC refinement CCP4 data scaling