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Crystal structure of pyridoxal kinase from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YXT PDB ENTRY 2YXT
Crystallization Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.21 α = 90 b = 80 β = 90 c = 106.39 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2009-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 50 92 0.05 23.7 4.8 18739 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 2.05 84.7 0.32 5.1 4.8
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 2YXT 2 19.71 18420 970 100 0.22171 0.2194 0.22 0.26537 0.2652 RANDOM 30.564
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] -1.33 -0.19 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.681 r_dihedral_angle_4_deg 20.086 r_dihedral_angle_3_deg 15.329 r_dihedral_angle_1_deg 6.142 r_scangle_it 2.343 r_scbond_it 1.561 r_mcangle_it 1.445 r_angle_refined_deg 1.307 r_angle_other_deg 0.856 r_mcbond_it 0.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.681 r_dihedral_angle_4_deg 20.086 r_dihedral_angle_3_deg 15.329 r_dihedral_angle_1_deg 6.142 r_scangle_it 2.343 r_scbond_it 1.561 r_mcangle_it 1.445 r_angle_refined_deg 1.307 r_angle_other_deg 0.856 r_mcbond_it 0.798 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_other 0.183 r_symmetry_vdw_refined 0.183 r_symmetry_vdw_other 0.181 r_nbd_other 0.177 r_nbtor_refined 0.172 r_mcbond_other 0.143 r_xyhbond_nbd_refined 0.141 r_nbtor_other 0.087 r_chiral_restr 0.069 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_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 2147 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing