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NlpC B3 - Trichomonas Vaginalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BIM 6BIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 1.26 M Ammonium Sulfate, 0.1 M Tris pH 8.5.
Crystal Properties Matthews coefficient Solvent content 2.17 38.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.05 α = 90 b = 34.05 β = 90 c = 181.449 γ = 90
Symmetry Space Group P 41 21 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 CCD ADSC QUANTUM 315 2016-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 1.3 33.47 99.94 0.01919 0.02714 0.01919 1 13.7 2 27581 12.09
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 1.3 1.32 99.51 0.3937 0.5568 0.3937 0.619 1.5 2
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 6BIM 1.3 33.47 26195 1386 99.94 0.14823 0.14713 0.1475 0.16827 0.1681 RANDOM 13.895
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.62 r_sphericity_free 21.553 r_dihedral_angle_4_deg 11.195 r_dihedral_angle_3_deg 9.736 r_sphericity_bonded 7.592 r_dihedral_angle_1_deg 5.771 r_long_range_B_refined 2.585 r_long_range_B_other 2.365 r_scangle_other 1.795 r_mcangle_it 1.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.62 r_sphericity_free 21.553 r_dihedral_angle_4_deg 11.195 r_dihedral_angle_3_deg 9.736 r_sphericity_bonded 7.592 r_dihedral_angle_1_deg 5.771 r_long_range_B_refined 2.585 r_long_range_B_other 2.365 r_scangle_other 1.795 r_mcangle_it 1.497 r_mcangle_other 1.497 r_scbond_it 1.385 r_scbond_other 1.384 r_angle_refined_deg 1.317 r_mcbond_it 1.186 r_mcbond_other 1.182 r_rigid_bond_restr 1.16 r_angle_other_deg 0.922 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 835 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing