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Crystal structure of apo Lin28B cold shock domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 2.5 M sodium acetate, 0.1 M HEPES , pH 7.0, EVAPORATION
Crystal Properties Matthews coefficient Solvent content 2.76 55.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.62 α = 90 b = 52.62 β = 90 c = 137.336 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 RAYONIX MX225HE 2010-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.98141 BESSY 14.1
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 1.06 32.3 99.5 0.056 0.056 17.8 100674 100170 2 2
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 1.06 1.087 98.3 0.61 0.61 2.8
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 pdb entry 312Z 1.06 32.3 100170 5027 100 0.1206 0.1196 0.1391 0.1467 RANDOM 15.9469
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] 0.11 0.06 0.11 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 12.272 r_scangle_it 6.783 r_dihedral_angle_1_deg 6.453 r_scbond_it 5.064 r_mcangle_it 4.259 r_mcbond_it 2.913 r_rigid_bond_restr 1.722 r_angle_refined_deg 1.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.36 r_dihedral_angle_4_deg 15.121 r_dihedral_angle_3_deg 12.272 r_scangle_it 6.783 r_dihedral_angle_1_deg 6.453 r_scbond_it 5.064 r_mcangle_it 4.259 r_mcbond_it 2.913 r_rigid_bond_restr 1.722 r_angle_refined_deg 1.573 r_mcbond_other 0.964 r_angle_other_deg 0.878 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1378 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 38
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction