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Crystal structure of apical membrane antigen 1 from Plasmodium vivax
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 THE CRYSTALLISATION MIXTURE CONSISTED OF 10-12% (W/V) PEG3350, 100-200MM IMIDAZOLE, PH 7.0, 5-10% (V/V) ISOPROPANOL, AND 1% (V/V) DMF OR 3% (V/V) T-BUTANOL. THE PROTEIN SOLUTION WAS DILUTED BY 40 - 60% WITH THE CRYSTALLISATION BUFFER, GIVING A FINAL CONCENTRATION OF 4-6 MG. ML-1 IN SUSPENDED DROPS OF VOLUME 2 - 3 PERCENT.
Crystal Properties Matthews coefficient Solvent content 2 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.097 α = 90 b = 76.096 β = 90 c = 103.925 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 CCD 2003-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 20 88.7 0.06 23.1 5.6 147056
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 2.07 53.4 0.32 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.01 20 24739 1347 88.7 0.198 0.194 0.1932 0.259 0.2568 RANDOM 39.02
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] -1.09 0.21 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.368 r_dihedral_angle_4_deg 19.701 r_dihedral_angle_3_deg 16.63 r_dihedral_angle_1_deg 7.332 r_scangle_it 5.642 r_scbond_it 3.987 r_mcangle_it 3.468 r_mcbond_it 2.142 r_angle_refined_deg 1.66 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.368 r_dihedral_angle_4_deg 19.701 r_dihedral_angle_3_deg 16.63 r_dihedral_angle_1_deg 7.332 r_scangle_it 5.642 r_scbond_it 3.987 r_mcangle_it 3.468 r_mcbond_it 2.142 r_angle_refined_deg 1.66 r_nbtor_refined 0.311 r_xyhbond_nbd_refined 0.242 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.227 r_chiral_restr 0.127 r_symmetry_hbond_refined 0.119 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_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 2935 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHARP phasing