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Crystal structure of Rhodostomin ARGDMP 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 293 0.2M (NH4)2SO4, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.78 55.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.499 α = 90 b = 61.334 β = 105.3 c = 34.644 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 ADSC QUANTUM 315 2019-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.00000 NSRRC BL13B1
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 1.8 30 99 0.115 18.1 4.2 14783
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 1.8 1.86 0.424
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 1.8 29.81 14043 740 98.95 0.22722 0.22342 0.218 0.3034 0.2864 RANDOM 18.049
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] 33.65 21.55 -14.98 -18.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.876 r_rigid_bond_restr 19.294 r_dihedral_angle_4_deg 18.155 r_dihedral_angle_3_deg 13.811 r_dihedral_angle_1_deg 7.53 r_long_range_B_refined 5.675 r_long_range_B_other 4.835 r_scangle_other 4.635 r_scbond_other 4.41 r_scbond_it 4.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.876 r_rigid_bond_restr 19.294 r_dihedral_angle_4_deg 18.155 r_dihedral_angle_3_deg 13.811 r_dihedral_angle_1_deg 7.53 r_long_range_B_refined 5.675 r_long_range_B_other 4.835 r_scangle_other 4.635 r_scbond_other 4.41 r_scbond_it 4.404 r_mcangle_other 3.238 r_mcangle_it 3.23 r_mcbond_it 2.739 r_mcbond_other 2.724 r_angle_refined_deg 1.486 r_angle_other_deg 1.381 r_chiral_restr 0.076 r_gen_planes_refined 0.015 r_bond_refined_d 0.012 r_bond_other_d 0.006 r_gen_planes_other 0.006 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 958 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing