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Ricin A-Chain (Recombinant) E177D Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IFT PDB ENTRY 1IFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.7 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.4 α = 90 b = 67.4 β = 90 c = 140.7 γ = 90
Symmetry Space Group P 41 21 2
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 2000-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 1.39 30 91.6 0.03 41.6 4 60577 -3 13.8
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 1.39 1.44 82.2 0.11 6.8 3.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IFT 1.39 29.49 58150 2427 92.1 0.183 0.182 0.1802 0.199 0.1974 RANDOM 16.92
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] 0.41 0.41 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.492 r_dihedral_angle_4_deg 22.138 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 5.203 r_scangle_it 4.101 r_scbond_it 2.69 r_mcangle_it 1.611 r_angle_refined_deg 1.419 r_mcbond_it 1.016 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.492 r_dihedral_angle_4_deg 22.138 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 5.203 r_scangle_it 4.101 r_scbond_it 2.69 r_mcangle_it 1.611 r_angle_refined_deg 1.419 r_mcbond_it 1.016 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.095 r_symmetry_hbond_refined 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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_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 2078 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing