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Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 277 20% of PEG 3350, 0.2 M ammonium tartrate dibasic, pH 6.6
Crystal Properties Matthews coefficient Solvent content 4.25 71.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.168 α = 90 b = 144.168 β = 90 c = 74.223 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS3 6M 2016-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97776 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 50 100 0.187 0.198 0.062 4.1 10.2 47259
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 99.7 0.803 0.857 0.293 0.833 8.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 2.7 35.6 44933 2250 99.85 0.1938 0.1916 0.1962 0.2385 0.2415 RANDOM 62.135
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] 0.96 0.48 0.96 -3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.236 r_dihedral_angle_4_deg 22.92 r_dihedral_angle_3_deg 18 r_dihedral_angle_1_deg 7.894 r_angle_refined_deg 1.813 r_angle_other_deg 1.374 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.236 r_dihedral_angle_4_deg 22.92 r_dihedral_angle_3_deg 18 r_dihedral_angle_1_deg 7.894 r_angle_refined_deg 1.813 r_angle_other_deg 1.374 r_chiral_restr 0.099 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3671 Nucleic Acid Atoms 2060 Solvent Atoms 271 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction SHELXCD phasing