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Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 22% PEG3350, 0.2 M Sodium malonate, 0.1 M BisTris
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.034 α = 90 b = 59.862 β = 94.55 c = 101.843 γ = 90
Symmetry Space Group P 1 21 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 2017-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 19.87 99.2 0.058 0.067 0.033 0.999 13.8 3.9 61417
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 2.05 99.3 0.738 0.847 0.411 0.9 4.1
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6bw3 2 19.87 58442 2961 99.09 0.2004 0.1987 0.2066 0.2333 0.242 RANDOM 52.505
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] 3.23 -0.31 -2.88 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.645 r_dihedral_angle_3_deg 13.215 r_dihedral_angle_4_deg 12.793 r_dihedral_angle_1_deg 6.796 r_angle_refined_deg 1.485 r_angle_other_deg 0.953 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.645 r_dihedral_angle_3_deg 13.215 r_dihedral_angle_4_deg 12.793 r_dihedral_angle_1_deg 6.796 r_angle_refined_deg 1.485 r_angle_other_deg 0.953 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5877 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 12
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing