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Crystal structure of Plasmodium falciparum glycerol kinase with bound glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BU6 PDB ENTRY 1BU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20% PEG 3350, 50 MM KFORMATE, 25 % ETHYLENE GLYCOL, 10 MM LDAO, 20 MM GLYCEROL, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.915 α = 90 b = 100.717 β = 92.56 c = 107.812 γ = 90
Symmetry Space Group P 1 21 1
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 CCD 2006-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.49 107.83 73.5 0.08 12 4.3 260542 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 1.49 1.53 18 0.63 2.23 3.4
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 1BU6 1.49 107.83 247410 13131 73.5 0.171 0.168 0.1605 0.21 0.2105 RANDOM 16.27
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] 1.07 0.08 -1 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.168 r_dihedral_angle_4_deg 19.923 r_dihedral_angle_3_deg 12.888 r_dihedral_angle_1_deg 6.026 r_scangle_it 3.987 r_scbond_it 2.696 r_mcangle_it 1.815 r_angle_refined_deg 1.389 r_mcbond_it 1.253 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.168 r_dihedral_angle_4_deg 19.923 r_dihedral_angle_3_deg 12.888 r_dihedral_angle_1_deg 6.026 r_scangle_it 3.987 r_scbond_it 2.696 r_mcangle_it 1.815 r_angle_refined_deg 1.389 r_mcbond_it 1.253 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.206 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 15930 Nucleic Acid Atoms Solvent Atoms 1929 Heterogen Atoms 320
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing