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Crystal structure of human ribonuclease 7 (RNase 7) in complex with 5'-adenosine monophosphate (5'-AMP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1M MIB (malonic acid:imidazole:boric acid = 2:3:3 molar ratio), pH 7.0, 25% w/v PEG 1.500
Crystal Properties Matthews coefficient Solvent content 2.23 44.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.11 α = 90 b = 48.17 β = 97.28 c = 62.9 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 PIXEL DECTRIS PILATUS3 6M 2022-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.1808 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.91 42.77 99.6 0.157 0.17 0.066 0.998 8.3 6.6 19968
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 1.97 98.6 5.029 5.532 2.271 0.242 0.3 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.07 42.76 1.33 15716 1573 99.5 0.2215 0.217 0.2182 0.2624 0.2628
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 f_dihedral_angle_d 19.33 f_angle_d 1.696 f_chiral_restr 0.078 f_bond_d 0.015 f_plane_restr 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2022 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 79
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing