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Crystal structure of Rhodostomin ARGDP 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 20% PEG4000, 0.2M Ammonium sulfate, 5% PEG3350, 2% PEG200, 0.5% 2-propanol(External) , pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.96 37.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.619 α = 106.839 b = 42.637 β = 103.858 c = 46.538 γ = 97.232
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 210 2013-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 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 1.8 30 96.7 0.059 23.9 3.7 19633
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 0.459
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.804 23.581 19631 961 96.481 0.161 0.157 0.1692 0.2332 0.2439 35.167
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] 1.327 0.031 1.39 -1.102 -0.61 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.818 r_dihedral_angle_3_deg 15.621 r_dihedral_angle_4_deg 12.739 r_dihedral_angle_1_deg 7.196 r_scangle_it 6.767 r_scangle_other 6.307 r_lrange_other 6.303 r_lrange_it 6.298 r_scbond_it 5.635 r_scbond_other 5.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.818 r_dihedral_angle_3_deg 15.621 r_dihedral_angle_4_deg 12.739 r_dihedral_angle_1_deg 7.196 r_scangle_it 6.767 r_scangle_other 6.307 r_lrange_other 6.303 r_lrange_it 6.298 r_scbond_it 5.635 r_scbond_other 5.239 r_mcangle_other 4.743 r_mcangle_it 4.741 r_mcbond_it 3.984 r_mcbond_other 3.98 r_rigid_bond_restr 2.606 r_angle_refined_deg 1.476 r_angle_other_deg 1.316 r_symmetry_nbd_refined 0.277 r_nbd_other 0.219 r_symmetry_nbd_other 0.2 r_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.187 r_xyhbond_nbd_other 0.162 r_xyhbond_nbd_refined 0.155 r_nbtor_refined 0.152 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1893 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing