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X-ray structure of the aquaglyceroporin from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FX8 PDB entry 1FX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 291 17% PEG MME 2000, 0.1M Sodium citrate, 15% Glycerol, 0.04M n-octyl-B-D-glucopyranoside, 0.01 Nickel sulfate, 0.01M DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.64 66.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.43 α = 90 b = 92.43 β = 90 c = 193.168 γ = 90
Symmetry Space Group I 4 2 2
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 2007-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.05 46.2 95.5 0.084 0.06 28.8 15 25478 24719 1 1 47.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 69.9 0.478 0.435 2.25 8.1 1819
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1FX8 2.05 46.2 1 1 24719 24179 1299 95.65 0.184 0.18175 0.18088 0.182 0.19824 0.2002 RANDOM 37.452
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] 1.51 1.51 -3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.083 r_dihedral_angle_4_deg 13.794 r_dihedral_angle_3_deg 13.646 r_dihedral_angle_1_deg 5.374 r_scangle_it 3.346 r_scbond_it 2.395 r_angle_refined_deg 1.628 r_mcangle_it 1.329 r_mcbond_it 0.854 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.083 r_dihedral_angle_4_deg 13.794 r_dihedral_angle_3_deg 13.646 r_dihedral_angle_1_deg 5.374 r_scangle_it 3.346 r_scbond_it 2.395 r_angle_refined_deg 1.628 r_mcangle_it 1.329 r_mcbond_it 0.854 r_nbtor_refined 0.318 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.218 r_symmetry_vdw_refined 0.19 r_chiral_restr 0.126 r_xyhbond_nbd_refined 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1853 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing