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Crystal structure of protein Ph1601p in complex with protein Ph1771p of archaeal ribonuclease P from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X0T 1X0T, 1V76 experimental model PDB 1V76 1X0T, 1V76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.4 20% PEG 3350, 0.2M KNO3, 50mM NaCl,50mM Tris-HCl , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K
Crystal Properties Matthews coefficient Solvent content 2.08 40.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.829 α = 90 b = 127.07 β = 90 c = 51.857 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 CCD RIGAKU JUPITER 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 98.6 0.064 0.064 33.8 6 25221 25221
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 89.6 0.369 0.369 3.15 5.4 1552
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1X0T, 1V76 2.21 42.64 23939 1273 98.52 0.20191 0.19938 0.25005 0.2653 RANDOM 36.98
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 -0.08 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.607 r_dihedral_angle_4_deg 19.117 r_dihedral_angle_3_deg 18.928 r_dihedral_angle_1_deg 6.285 r_scangle_it 2.46 r_scbond_it 1.606 r_angle_refined_deg 1.397 r_mcangle_it 1.104 r_mcbond_it 0.651 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.607 r_dihedral_angle_4_deg 19.117 r_dihedral_angle_3_deg 18.928 r_dihedral_angle_1_deg 6.285 r_scangle_it 2.46 r_scbond_it 1.606 r_angle_refined_deg 1.397 r_mcangle_it 1.104 r_mcbond_it 0.651 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.111 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3365 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing