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Crystal structures of FMN-free form of dihydroorotate dehydrogenase from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1 M Sodium Citrate buffer, 1.5-2.5 M Sodium Malonate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.053 α = 90 b = 146.218 β = 90 c = 66.389 γ = 90
Symmetry Space Group P 21 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 95 CCD ADSC QUANTUM 210 2013-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 40 99.4 33.7 13.3 180934
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 1.6 1.63 97.5 2.5
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 2B4G 1.6 36.95 169835 8964 99.39 0.17544 0.1745 0.1863 0.1931 0.2038 RANDOM 21.679
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.532 r_dihedral_angle_4_deg 14.976 r_dihedral_angle_3_deg 11.136 r_dihedral_angle_1_deg 5.892 r_long_range_B_refined 4.116 r_long_range_B_other 3.918 r_scangle_other 2.171 r_mcangle_other 1.383 r_mcangle_it 1.382 r_scbond_it 1.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.532 r_dihedral_angle_4_deg 14.976 r_dihedral_angle_3_deg 11.136 r_dihedral_angle_1_deg 5.892 r_long_range_B_refined 4.116 r_long_range_B_other 3.918 r_scangle_other 2.171 r_mcangle_other 1.383 r_mcangle_it 1.382 r_scbond_it 1.355 r_scbond_other 1.355 r_angle_refined_deg 1.242 r_angle_other_deg 0.907 r_mcbond_it 0.839 r_mcbond_other 0.837 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9589 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing