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Arabidopsis thaliana nuclear protein-only RNase P 2 (PRORP2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G26 PDB ENTRY 4G26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6 277 PRORP2 STOCK SOLUTION WAS PREPARED AT 2.5 MG/ML IN 50 MM HEPES-NA PH 7.5, 250 MM NACL, 5%(W/V) GLYCEROL, 1 MM TCEP. PRORP2 WAS CRYSTALLIZED AT 277 K IN 2 MICROLITER MICROBATCH DROPS SET UP UNDER PARAFIN OIL BY MIXING 1 VOLUME OF PRORP2 SOLUTION WITH 1 VOLUME OF CRYSTALLANT SOLUTION CONTAINING 200 MM SODIUM MALONATE PH 6, 20% (W/V) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.9 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.5 α = 63.1 b = 72.8 β = 72.2 c = 80.3 γ = 78.4
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 PILATUS 2M 2013-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 3.05 35 92.4 0.12 8.7 3.5 23923 -3 93.61
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 3.05 3.23 98.2 1.5 0.8 3.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 PDB ENTRY 4G26 3.05 34.707 1.91 23727 1126 92.2 0.2444 0.2421 0.2539 0.2897 0.3003 145.9
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 15.092 f_angle_d 1.148 f_chiral_restr 0.051 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7442 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing