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Crystal Structure of Mini-ribonuclease 3 from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.2M sodium acetate trihydrate, 0.1M TRIS, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.55 20.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.092 α = 90 b = 62.028 β = 90 c = 89.388 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.917152 BESSY 14.1
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 44.7 99.8 0.091 17.17 10956 10939 2 36.163
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 99.3 1.4 1.468 2.04
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1U61 1.8 44.69 2 10956 10939 547 99.84 0.2092 0.206 0.2676 0.2538 RANDOM 41.917
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] 0.05 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.582 r_dihedral_angle_4_deg 29.895 r_dihedral_angle_3_deg 15.358 r_dihedral_angle_1_deg 6.042 r_scbond_it 5.046 r_mcangle_it 4.816 r_mcbond_it 3.387 r_angle_refined_deg 1.542 r_chiral_restr 0.114 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.582 r_dihedral_angle_4_deg 29.895 r_dihedral_angle_3_deg 15.358 r_dihedral_angle_1_deg 6.042 r_scbond_it 5.046 r_mcangle_it 4.816 r_mcbond_it 3.387 r_angle_refined_deg 1.542 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1009 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction