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STRUCTURE OF THE D121N VARIANT OF RIBONUCLEASE A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RPH PDB ENTRY 1RPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch method 5.2 LYOPHILIZED D121N RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ ML. CRYSTALLIZATION WAS PERFORMED IN SMALL SILICONIZED TUBES USING THE BATCH METHOD. A SOLUTION (25UL) OF THE ENZYME WAS MIXED WITH AN EQUAL VOLUME OF 95% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.10 M MES BUFFER, PH 5.2. CRYSTALS APPEARED WITHIN SEVERAL MONTHS., batch method
Crystal Properties Matthews coefficient Solvent content 2.19 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.52 α = 90 b = 38.4 β = 105.7 c = 53.31 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 277 AREA DETECTOR SIEMENS LONG MIRRORS 1995-08-28 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 30 88 0.019 31 1.8 15756 0.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.7 75 0.057
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1RPH 1.6 30 15756 15756 88 0.177
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]
RMS Deviations Key Refinement Restraint Deviation t_dihedral_angle_d 17.1 t_angle_deg 2.15 t_it 1 t_nbd 0.026 t_bond_d 0.011 t_gen_planes 0.009 t_trig_c_planes 0.005 t_incorr_chiral_ct t_pseud_angle
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 956 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling XCALIBRE data reduction AMoRE phasing TNT refinement XDS data reduction XCALIBRE data scaling