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Crystal Structure of Plasmodium yoelii Multidrug Resistance Protein 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 297 29%Peg 3350, 0.2M Li2SO4, 4% Glycerol, and 0.1M BisTris pH 5.5 , VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.015 α = 69.81 b = 70.689 β = 76.69 c = 74.384 γ = 82.29
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++ VariMax HR 2006-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54
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 2.2 50 99.9 0.1 0.1 8 5.2 56948 56948 43.6
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) 2.2 2.24 100 0.67 0.67 1.77 4.9 2824
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 1MV5 2.2 32.67 56088 56087 857 99.06 0.20568 0.20568 0.20448 0.2035 0.28834 0.2818 RANDOM 44.88
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] -0.28 0.62 0.1 0.55 -0.42 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.137 r_dihedral_angle_4_deg 20.632 r_dihedral_angle_3_deg 19.327 r_dihedral_angle_1_deg 7.161 r_scangle_it 3.849 r_scbond_it 2.573 r_angle_refined_deg 1.881 r_mcangle_it 1.6 r_mcbond_it 0.969 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.137 r_dihedral_angle_4_deg 20.632 r_dihedral_angle_3_deg 19.327 r_dihedral_angle_1_deg 7.161 r_scangle_it 3.849 r_scbond_it 2.573 r_angle_refined_deg 1.881 r_mcangle_it 1.6 r_mcbond_it 0.969 r_nbtor_refined 0.31 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.21 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.13 r_bond_refined_d 0.019 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 7551 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling PHASER phasing Coot model building