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Ribosome inactivating protein type 1 from Charybdis maritima AGG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other combined model from PARTS OF 12 RIP's
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 283 100mM Mes, 16% PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.24 α = 90 b = 57.24 β = 104.08 c = 51.088 γ = 90
Symmetry Space Group C 1 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 2005-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.6 49.63 97 0.064 0.064 18.1 4.6 35616 18.86
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) 1.6 1.69 82.2 0.186 0.186 5.9 3.2
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 (All) 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 combined model from PARTS OF 12 RIP's 1.6 20 33815 1785 97.2 0.18648 0.183 0.182 0.208 0.2617 RANDOM 18.21
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] -0.74 -0.42 0.37 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.882 r_dihedral_angle_4_deg 23.992 r_dihedral_angle_3_deg 15.362 r_dihedral_angle_1_deg 5.496 r_scangle_it 3.565 r_scbond_it 2.446 r_mcangle_it 1.669 r_angle_refined_deg 1.598 r_mcbond_it 1.123 r_angle_other_deg 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.882 r_dihedral_angle_4_deg 23.992 r_dihedral_angle_3_deg 15.362 r_dihedral_angle_1_deg 5.496 r_scangle_it 3.565 r_scbond_it 2.446 r_mcangle_it 1.669 r_angle_refined_deg 1.598 r_mcbond_it 1.123 r_angle_other_deg 0.886 r_mcbond_other 0.235 r_symmetry_vdw_other 0.231 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.22 r_nbd_other 0.194 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.163 r_symmetry_hbond_refined 0.085 r_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2047 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 12
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling