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Trypanosoma brucei CTPS - glutaminase domain with bound acivicin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VCN PDB ENTRY 1VCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.15 M POTASSIUM BROMIDE, 30 % PEG MONOMETHYL ETHER 2000
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.48 α = 90 b = 63.68 β = 90 c = 76.58 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 315 MIRRORS 2008-12-11 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 2.1 20 99.1 0.08 13.9 7.84 14866 2
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 2.1 2.15 93.4 0.22 6.16 5.97
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 1VCN 2.1 19.78 14121 744 100 0.202 0.199 0.2025 0.262 0.2644 RANDOM 14.1
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] -0.37 1.11 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.974 r_dihedral_angle_4_deg 18.988 r_dihedral_angle_3_deg 14.971 r_dihedral_angle_1_deg 5.615 r_scangle_it 2.844 r_scbond_it 1.875 r_mcangle_it 1.311 r_angle_refined_deg 1.254 r_angle_other_deg 0.911 r_mcbond_it 0.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.974 r_dihedral_angle_4_deg 18.988 r_dihedral_angle_3_deg 14.971 r_dihedral_angle_1_deg 5.615 r_scangle_it 2.844 r_scbond_it 1.875 r_mcangle_it 1.311 r_angle_refined_deg 1.254 r_angle_other_deg 0.911 r_mcbond_it 0.883 r_symmetry_vdw_other 0.216 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.199 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.174 r_symmetry_vdw_refined 0.142 r_nbtor_other 0.094 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 2072 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing