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Crystal structure of human Ribosomal protein L10 core domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S72 PDB ENTRY 1S72 chain H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 1.0M di-sodium hydroxyl phosphate, 1.0M potassium dihydroxyl phosphate, pH 4.5 100mM sodium acetate , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.16 43.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.724 α = 90 b = 52.724 β = 90 c = 185.489 γ = 120
Symmetry Space Group P 31 2 1
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 ADSC QUANTUM 315 rhodium-coated mirrors 2006-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 2.5 50 98.1 0.05 36.6 5.9 10870 -3 60
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) 2.5 2.59 97 0.438 3.62 5.9 1019
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1S72 chain H 2.5 45.66 10814 567 98.1 0.24 0.24 0.2411 0.264 RANDOM 56.4
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] 11.58 7.78 11.58 -23.16
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_angle_deg 1.2 c_improper_angle_d 0.74 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_angle_deg 1.2 c_improper_angle_d 0.74 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1750 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing