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Crystal structure of a coiled-coil domain from human THAP11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N6M PDB ENTRY 1N6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 285 0.1 M NA/K PHOSPHATE PH 6.2, 0.2 M NACL, 40% (V/V) MPD, HANGING DROP VAPOUR DIFFUSION, T = 285 K
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.757 α = 90 b = 39.757 β = 90 c = 204.127 γ = 90
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 PILATUS 6M TOROIDAL MIRROR 2014-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.3 39.76 99.4 0.04 16.2 3.8 13992 -3 52.3
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 2.3 2.38 97.8 0.44 2.6 3.8
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 1N6M 2.3 39.76 13209 737 99.43 0.21236 0.207 0.2212 0.29516 0.3145 THIN SHELLS 78.591
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] 32.55 32.55 -65.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.251 r_dihedral_angle_4_deg 23.848 r_dihedral_angle_3_deg 19.134 r_mcangle_it 9.989 r_scbond_it 8.9 r_mcbond_other 7.582 r_mcbond_it 7.58 r_dihedral_angle_1_deg 5.775 r_angle_refined_deg 1.708 r_angle_other_deg 0.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.251 r_dihedral_angle_4_deg 23.848 r_dihedral_angle_3_deg 19.134 r_mcangle_it 9.989 r_scbond_it 8.9 r_mcbond_other 7.582 r_mcbond_it 7.58 r_dihedral_angle_1_deg 5.775 r_angle_refined_deg 1.708 r_angle_other_deg 0.827 r_chiral_restr 0.078 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_it 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 1880 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing