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HBZ56 in complex with KIX and c-Myb
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AGH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350, ammonium iodide
Crystal Properties Matthews coefficient Solvent content 2.04 39.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.997 α = 90 b = 80.311 β = 92.6 c = 64.641 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 PIXEL DECTRIS PILATUS3 S 6M 2016-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 50 95.2 16.6 6 13196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9
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 2AGH 2.8 40.97 12521 660 94.57 0.24198 0.23871 0.2395 0.30083 0.3049 RANDOM 94.383
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] -1.7 0.3 4.76 -3.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.661 r_dihedral_angle_4_deg 20.25 r_dihedral_angle_3_deg 19.305 r_long_range_B_refined 14.612 r_long_range_B_other 14.611 r_scangle_other 10.499 r_mcangle_it 9.587 r_mcangle_other 9.585 r_scbond_it 6.448 r_scbond_other 6.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.661 r_dihedral_angle_4_deg 20.25 r_dihedral_angle_3_deg 19.305 r_long_range_B_refined 14.612 r_long_range_B_other 14.611 r_scangle_other 10.499 r_mcangle_it 9.587 r_mcangle_other 9.585 r_scbond_it 6.448 r_scbond_other 6.447 r_mcbond_it 6.091 r_mcbond_other 6.089 r_dihedral_angle_1_deg 4.841 r_angle_refined_deg 1.056 r_angle_other_deg 0.41 r_chiral_restr 0.039 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4187 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing