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Crystal Structure of the Nicotiana glutinosa Ribonuclease NW
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 8.5 291.15 ammonium dihydrogen, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 2.24 45.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.8 α = 90 b = 94.3 β = 90 c = 98.1 γ = 90
Symmetry Space Group P 21 21 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 CCD OXFORD PX210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.5 37.43 93.2 0.052 28.6 5.6 62367 1 1 14.6
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) 1.5 1.55 53.8 0.201 2.7 1.7 3581
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-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 1.5 37.41 62367 62367 3152 92.5 0.212 0.2038 0.23 0.2204 RANDOM 13
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] 0.61 -1.08 0.48
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 2.77 c_scbond_it 1.91 c_mcangle_it 1.49 c_angle_deg 1.4 c_mcbond_it 1.01 c_improper_angle_d 0.89 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3258 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 48
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction CNS refinement CNS phasing