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Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G24 4G24, 1EHZ experimental model PDB 1EHZ 4G24, 1EHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 1.5 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 4.48 72.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.48 α = 90 b = 131.701 β = 90 c = 155.556 γ = 90
Symmetry Space Group P 21 21 2
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 2017-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.85 50 99.9 0.124 0.055 13.8 5 42492
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9 100 1.075 0.48 0.792 1.56 4.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4G24, 1EHZ 2.85 49.312 41250 2087 99.821 0.236 0.2347 0.2261 0.2554 0.2452 120.68
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] 0.223 -1.877 1.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.575 r_dihedral_angle_4_deg 25.43 r_dihedral_angle_3_deg 19.879 r_rigid_bond_restr 15.104 r_lrange_other 4.463 r_lrange_it 4.41 r_dihedral_angle_1_deg 4.302 r_scangle_it 3.068 r_scangle_other 3.067 r_angle_other_deg 2.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.575 r_dihedral_angle_4_deg 25.43 r_dihedral_angle_3_deg 19.879 r_rigid_bond_restr 15.104 r_lrange_other 4.463 r_lrange_it 4.41 r_dihedral_angle_1_deg 4.302 r_scangle_it 3.068 r_scangle_other 3.067 r_angle_other_deg 2.249 r_scbond_other 2.081 r_mcangle_other 1.952 r_mcangle_it 1.918 r_scbond_it 1.818 r_angle_refined_deg 1.606 r_mcbond_other 1.192 r_mcbond_it 1.137 r_symmetry_xyhbond_nbd_refined 0.26 r_symmetry_nbd_other 0.257 r_nbd_other 0.232 r_nbtor_refined 0.209 r_xyhbond_nbd_refined 0.177 r_nbd_refined 0.175 r_symmetry_nbd_refined 0.15 r_chiral_restr 0.124 r_symmetry_xyhbond_nbd_other 0.105 r_symmetry_nbtor_other 0.08 r_bond_other_d 0.028 r_bond_refined_d 0.027 r_gen_planes_refined 0.023 r_gen_planes_other 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3055 Nucleic Acid Atoms 3136 Solvent Atoms 35 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing