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Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 20% PEG3350, 0.2 M sodium malonate, 0.1 M BisTris
Crystal Properties Matthews coefficient Solvent content 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.979 α = 90 b = 59.822 β = 94.55 c = 101.773 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 RIGAKU SATURN A200 2017-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 2.2 46.95 99.4 0.099 0.114 0.056 0.99 14.3 4.1 46303
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 2.27 98.4 0.991 1.141 0.559 0.681 4
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 MOLECULAR REPLACEMENT THROUGHOUT 2xu7 2.2 46.95 44059 2217 99.3 0.21671 0.21521 0.2215 0.24594 0.2517 RANDOM 43.608
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] 0.05 0.43 -0.82 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.885 r_dihedral_angle_3_deg 14.216 r_dihedral_angle_4_deg 12.841 r_dihedral_angle_1_deg 6.931 r_long_range_B_refined 3.312 r_long_range_B_other 3.305 r_angle_refined_deg 1.476 r_angle_other_deg 0.965 r_mcangle_it 0.94 r_mcangle_other 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.885 r_dihedral_angle_3_deg 14.216 r_dihedral_angle_4_deg 12.841 r_dihedral_angle_1_deg 6.931 r_long_range_B_refined 3.312 r_long_range_B_other 3.305 r_angle_refined_deg 1.476 r_angle_other_deg 0.965 r_mcangle_it 0.94 r_mcangle_other 0.94 r_scangle_other 0.695 r_mcbond_it 0.536 r_mcbond_other 0.536 r_scbond_it 0.417 r_scbond_other 0.417 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5841 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing