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Crystal structure of Trypanosoma brucei Morn1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T4D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295.15 0.166 M Tris-HCl pH 8.8, 0.15 M MgCl2, 0.45 M KI, 24% PEG 2000 MME, and 4% glycerol
Crystal Properties Matthews coefficient Solvent content 2.17 43.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.039 α = 90 b = 27.63 β = 101.833 c = 114.542 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 PILATUS 6M 2013-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.35 48.28 95.4 0.092 0.1 0.04 0.998 13.4 6.1 17460 18.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 71.5 0.466 0.532 0.25 0.897 2.8 4.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6T4D 2.352 48.28 17452 818 95.231 0.223 0.2209 0.2211 0.259 0.2586 35.095
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] -1.493 -4.491 -1.163 4.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.529 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_4_deg 16.071 r_lrange_it 7.396 r_lrange_other 7.385 r_dihedral_angle_1_deg 7.352 r_scangle_it 5.573 r_scangle_other 5.573 r_mcangle_other 4.449 r_mcangle_it 4.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.529 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_4_deg 16.071 r_lrange_it 7.396 r_lrange_other 7.385 r_dihedral_angle_1_deg 7.352 r_scangle_it 5.573 r_scangle_other 5.573 r_mcangle_other 4.449 r_mcangle_it 4.446 r_scbond_it 3.596 r_scbond_other 3.596 r_mcbond_it 2.881 r_mcbond_other 2.867 r_angle_other_deg 2.435 r_angle_refined_deg 1.258 r_symmetry_xyhbond_nbd_other 0.282 r_symmetry_nbd_refined 0.219 r_nbd_other 0.214 r_symmetry_nbd_other 0.201 r_nbd_refined 0.182 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.089 r_symmetry_nbtor_other 0.067 r_chiral_restr 0.044 r_bond_other_d 0.037 r_gen_planes_other 0.006 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3404 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing