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Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana after overnight soak with juglone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G23 PDB ENTRY 4G23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 18% PEG3350, 0.1 M sodium citrate tribasic, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.89 57.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.78 α = 90 b = 111.818 β = 90 c = 139.34 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 PIXEL DECTRIS EIGER X 16M K-B pair of biomorph mirrors for vertical and horizontal focusing 2017-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.1 87.21 100 0.055 17.5 6.7 39128 37
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 2.1 2.16 99.7 0.717 2.2 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4G23 2.1 87.21 37078 1982 100 0.198 0.196 0.1975 0.241 0.2427 RANDOM 63.12
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] -0.23 1.54 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.389 r_dihedral_angle_4_deg 17.785 r_dihedral_angle_3_deg 14.963 r_long_range_B_refined 8.457 r_long_range_B_other 8.434 r_scangle_other 6.153 r_dihedral_angle_1_deg 6.12 r_mcangle_other 5.489 r_mcangle_it 5.486 r_scbond_it 4.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.389 r_dihedral_angle_4_deg 17.785 r_dihedral_angle_3_deg 14.963 r_long_range_B_refined 8.457 r_long_range_B_other 8.434 r_scangle_other 6.153 r_dihedral_angle_1_deg 6.12 r_mcangle_other 5.489 r_mcangle_it 5.486 r_scbond_it 4.035 r_scbond_other 4.035 r_mcbond_it 3.844 r_mcbond_other 3.836 r_angle_refined_deg 1.449 r_angle_other_deg 0.921 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3766 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing