☰ Navigation Tabs
The NF-Y transcription factor is structurally and functionally a sequence specific histone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N1J PDB ENTRY 1N1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 VAPOUR DIFFUSION METHOD , HANGING DROP, 20-24% PEG3350, 100 MM MES OR CACODYLATE BUFFER, PH 6.5, 50 MM NAF. T ROOM.
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.7 α = 90 b = 62.56 β = 90 c = 139.68 γ = 90
Symmetry Space Group P 21 21 21
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 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9,1.0 ESRF ID29
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 3.08 62.56 94.9 0.06 17.4 5.2 8907 3
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) 1 3.08 3.25 76.9 0.17 4.4 3.5
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 PDB ENTRY 1N1J 3.08 35.46 8448 418 100 0.19418 0.19133 0.1986 0.24971 0.2511 RANDOM 79.475
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] 8.15 -0.55 -7.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.568 r_dihedral_angle_3_deg 23.756 r_dihedral_angle_4_deg 18.478 r_dihedral_angle_1_deg 5.831 r_scangle_it 1.969 r_angle_refined_deg 1.751 r_scbond_it 1.183 r_mcangle_it 0.853 r_mcbond_it 0.42 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.568 r_dihedral_angle_3_deg 23.756 r_dihedral_angle_4_deg 18.478 r_dihedral_angle_1_deg 5.831 r_scangle_it 1.969 r_angle_refined_deg 1.751 r_scbond_it 1.183 r_mcangle_it 0.853 r_mcbond_it 0.42 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1928 Nucleic Acid Atoms 1019 Solvent Atoms 2 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing