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Crystal Structure of a deletion mutant of human Reverba ligand binding domain bound with an NCoR ID1 peptide determined to 2.60A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 295 1ul of precipitant composed of 6-9% of PEG 3350, 8% glycerol, 200mM proline, 80mM HEPES was mixed with 1uL of the Rev-erba NCoR complex at 5-6 mG/Lit to obtain diffraction grade crystals, pH 7.5, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.1 41.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.55 α = 90 b = 112.55 β = 90 c = 103.833 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 100 CCD MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.6 50 99.9 0.049 50.5 10.9 7931 7921 -3 32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.69 99.4 0.296 7.3 9.8 783
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 1db1 2.6 30.04 7693 225 99.86 0.20035 0.19861 0.2028 0.26633 0.2698 RANDOM 39.146
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.156 r_dihedral_angle_4_deg 22.934 r_dihedral_angle_3_deg 15.115 r_dihedral_angle_1_deg 5.433 r_scangle_it 2.9 r_scbond_it 1.591 r_mcangle_it 1.184 r_angle_refined_deg 1.126 r_angle_other_deg 0.837 r_mcbond_it 0.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.156 r_dihedral_angle_4_deg 22.934 r_dihedral_angle_3_deg 15.115 r_dihedral_angle_1_deg 5.433 r_scangle_it 2.9 r_scbond_it 1.591 r_mcangle_it 1.184 r_angle_refined_deg 1.126 r_angle_other_deg 0.837 r_mcbond_it 0.604 r_mcbond_other 0.067 r_chiral_restr 0.055 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1549 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms
Software Software Software Name Purpose JDirector data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling