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Crystal Structure Analysis of Human RNase T2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DIX PDB ENTRY 1DIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 15% PEG3350, 0.2 M ammonium nitrate, macroseeding, no buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.797959 31.589108
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.2 α = 90 b = 67.4 β = 90.81 c = 47.9 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX-225 2011-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184,0.9810 BESSY 14.1
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 1.585 28.31 98 0.0632 0.0632 171 5.91 26985 26433 -3 -3 24.34
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 1.59 1.69 0.1914 0.1914 5.04 2.55 4246
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1DIX 1.59 27.56 25576 25064 1347 98 0.15378 0.15182 0.1753 0.19033 0.2101 RANDOM 18.886
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] -0.43 0.2 1.03 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.787 r_dihedral_angle_4_deg 20.752 r_dihedral_angle_3_deg 12.682 r_dihedral_angle_1_deg 6.151 r_scangle_it 4.845 r_scbond_it 3.137 r_mcangle_it 2.167 r_angle_refined_deg 2.057 r_mcbond_it 1.294 r_chiral_restr 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.787 r_dihedral_angle_4_deg 20.752 r_dihedral_angle_3_deg 12.682 r_dihedral_angle_1_deg 6.151 r_scangle_it 4.845 r_scbond_it 3.137 r_mcangle_it 2.167 r_angle_refined_deg 2.057 r_mcbond_it 1.294 r_chiral_restr 0.142 r_bond_refined_d 0.021 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1599 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 28
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement XDS data reduction SADABS data scaling