☰ Navigation Tabs
Crystal structure of Trypanosoma brucei macrodomain (crystal form 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IQY PDB ENTRY 4IQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M SODIUM SULFATE, 0.1 M BIS-TRIS PROPANE PH 7.5, 20 % W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.16 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.14 α = 90 b = 77.14 β = 90 c = 427.45 γ = 120
Symmetry Space Group P 61 2 2
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 PIXEL MIRRORS 2015-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.95 30 99.7 0.09 16.9 15.1 56483 -3
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 1.95 2 99.7 1.8 15.1
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 4IQY 1.95 19.75 53658 2825 99.75 0.19042 0.18889 0.1991 0.21912 0.2287 RANDOM 53.727
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] 1.54 0.77 1.54 -4.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.719 r_dihedral_angle_4_deg 18.274 r_dihedral_angle_3_deg 12.704 r_dihedral_angle_1_deg 6.035 r_mcangle_it 4.068 r_scbond_it 3.771 r_mcbond_other 2.941 r_mcbond_it 2.94 r_angle_refined_deg 1.43 r_angle_other_deg 0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.719 r_dihedral_angle_4_deg 18.274 r_dihedral_angle_3_deg 12.704 r_dihedral_angle_1_deg 6.035 r_mcangle_it 4.068 r_scbond_it 3.771 r_mcbond_other 2.941 r_mcbond_it 2.94 r_angle_refined_deg 1.43 r_angle_other_deg 0.918 r_chiral_restr 0.083 r_bond_refined_d 0.011 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 3649 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing