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Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana, SeMet substituted form with Sr
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% PEG 3,350, 0.1 M sodium citrate pH 5.5, and 0.02 M SrCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.86 57.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.844 α = 90 b = 111.814 β = 90 c = 140.226 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 CCD MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2012-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.968 APS 23-ID-D
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 2 50 98.4 0.084 12.6 5.4 45501 44773
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 2 2.07 97.9 0.63 2.6 5.4 4456
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 33.5 44733 42464 2269 98.4 0.19606 0.19405 0.2011 0.23354 0.2371 RANDOM 44.137
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] 0.17 1.6 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.483 r_dihedral_angle_4_deg 21.697 r_dihedral_angle_3_deg 14.589 r_dihedral_angle_1_deg 6.119 r_angle_refined_deg 1.552 r_angle_other_deg 1.128 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.483 r_dihedral_angle_4_deg 21.697 r_dihedral_angle_3_deg 14.589 r_dihedral_angle_1_deg 6.119 r_angle_refined_deg 1.552 r_angle_other_deg 1.128 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3787 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 2
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling