☰ Navigation Tabs
Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TCS PDB ENTRY 1TCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7% PEG 20000, 0.1M MES, PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.589 α = 90 b = 43.964 β = 92.87 c = 92.235 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 100 IMAGE PLATE RIGAKU IMAGE PLATE VARIMAX HR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2.2 92 99.4 0.1 9.6 2.4 24055 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) 1 2.2 2.32 98 0.26 3.2 2.4
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TCS 2.2 25.47 24055 1283 98 0.167 0.163 0.238 0.2169 RANDOM 19.34
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] -0.6 1.79 -0.46 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.129 r_dihedral_angle_4_deg 20.772 r_dihedral_angle_3_deg 16.789 r_dihedral_angle_1_deg 7.161 r_scangle_it 4.116 r_scbond_it 2.917 r_angle_refined_deg 2.068 r_mcangle_it 1.805 r_mcbond_it 1.494 r_angle_other_deg 1.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.129 r_dihedral_angle_4_deg 20.772 r_dihedral_angle_3_deg 16.789 r_dihedral_angle_1_deg 7.161 r_scangle_it 4.116 r_scbond_it 2.917 r_angle_refined_deg 2.068 r_mcangle_it 1.805 r_mcbond_it 1.494 r_angle_other_deg 1.033 r_symmetry_vdw_other 0.251 r_nbd_refined 0.198 r_nbd_other 0.193 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.131 r_symmetry_hbond_refined 0.13 r_symmetry_vdw_refined 0.104 r_nbtor_other 0.094 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 3978 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing