☰ Navigation Tabs
Crystal structure of Rhodostomin ARGDWP mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Tris pH 8.5, 2M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.09 41.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.709 α = 90 b = 79.281 β = 90 c = 92.011 γ = 90
Symmetry Space Group F 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD ADSC QUANTUM 315 2019-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1.00000 NSRRC BL13C1
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 1.48 30 99.8 0.07 28.8 7 20726
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 1.48 1.53 0.714
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 4RQG 1.48 23.8 19620 1103 99.83 0.1652 0.1625 0.1717 0.21392 0.2252 RANDOM 18.683
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] -0.44 0.11 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.734 r_dihedral_angle_4_deg 12.266 r_dihedral_angle_3_deg 11.042 r_dihedral_angle_1_deg 6.06 r_scangle_other 3.729 r_long_range_B_refined 3.372 r_long_range_B_other 3.307 r_scbond_other 3.093 r_scbond_it 3.074 r_rigid_bond_restr 2.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.734 r_dihedral_angle_4_deg 12.266 r_dihedral_angle_3_deg 11.042 r_dihedral_angle_1_deg 6.06 r_scangle_other 3.729 r_long_range_B_refined 3.372 r_long_range_B_other 3.307 r_scbond_other 3.093 r_scbond_it 3.074 r_rigid_bond_restr 2.664 r_mcangle_it 2.389 r_mcangle_other 2.387 r_mcbond_it 1.93 r_mcbond_other 1.927 r_angle_refined_deg 1.491 r_angle_other_deg 1.482 r_chiral_restr 0.075 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 982 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing