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Crystal structure of trypanosoma brucei gambiense glycerol kinase (ligand-free form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W40 PDB ENTRY 2W40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20-30% PEG 400, 0.1M HEPES, 0.01M MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.95 58.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.763 α = 90 b = 131.979 β = 90 c = 148.613 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 270 2010-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 2.9 50 99.6 0.05 19.4 30649 29027 -3
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 2.9 2.95 99.6 0.675 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2W40 2.9 30 30649 29027 1539 99.51 0.21 0.20596 0.20183 0.2547 0.28208 0.3124 RANDOM 66.885
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] -3.45 2.48 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_4_deg 22.377 r_dihedral_angle_3_deg 21.938 r_dihedral_angle_1_deg 7.206 r_scangle_it 2.635 r_angle_refined_deg 1.59 r_scbond_it 1.536 r_mcangle_it 1.199 r_mcbond_it 0.629 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_4_deg 22.377 r_dihedral_angle_3_deg 21.938 r_dihedral_angle_1_deg 7.206 r_scangle_it 2.635 r_angle_refined_deg 1.59 r_scbond_it 1.536 r_mcangle_it 1.199 r_mcbond_it 0.629 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7897 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling