Plasmodium falciparum lipocalin (PF3D7_0925900)
X-RAY DIFFRACTION - SOLUTION SCATTERING
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION | 7 | 292 | 0.2 M magnesium chloride, 0.1 M Tris pH7, 2.5 M Sodium Chloride |
Crystal Properties |
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Matthews coefficient | Solvent content |
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3.7 | 66.76 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 63.993 | α = 90 |
b = 92.25 | β = 98.35 |
c = 214.502 | γ = 90 |
Symmetry |
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Space Group | I 1 2 1 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | | 2019-03-05 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9762 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 |
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1 | 2.85 | 56.2 | 99.75 | 0.1985 | | 0.2943 | | 0.546 | | 3.69 | 2 | | 28936 | | | 54.95 |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2.85 | 2.952 | | | | | | 0.41 | | 1.19 | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | 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 | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.85 | 56.2 | | | | 27535 | 1428 | 99.75 | | 0.1912 | 0.18886 | 0.23647 | RANDOM | 53.494 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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-0.09 | | -0.04 | 0.09 | | 0.01 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 41.265 |
r_dihedral_angle_4_deg | 19.276 |
r_dihedral_angle_3_deg | 17.812 |
r_long_range_B_other | 11.251 |
r_long_range_B_refined | 11.234 |
r_dihedral_angle_1_deg | 9.775 |
r_scangle_other | 7.468 |
r_mcangle_other | 6.898 |
r_mcangle_it | 6.895 |
r_scbond_it | 4.654 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 41.265 |
r_dihedral_angle_4_deg | 19.276 |
r_dihedral_angle_3_deg | 17.812 |
r_long_range_B_other | 11.251 |
r_long_range_B_refined | 11.234 |
r_dihedral_angle_1_deg | 9.775 |
r_scangle_other | 7.468 |
r_mcangle_other | 6.898 |
r_mcangle_it | 6.895 |
r_scbond_it | 4.654 |
r_scbond_other | 4.604 |
r_mcbond_it | 4.33 |
r_mcbond_other | 4.313 |
r_angle_refined_deg | 1.539 |
r_angle_other_deg | 1.208 |
r_chiral_restr | 0.064 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
r_nbd_refined | |
r_nbd_other | |
r_nbtor_refined | |
r_nbtor_other | |
r_xyhbond_nbd_refined | |
r_xyhbond_nbd_other | |
r_metal_ion_refined | |
r_metal_ion_other | |
r_symmetry_vdw_refined | |
r_symmetry_vdw_other | |
r_symmetry_hbond_refined | |
r_symmetry_hbond_other | |
r_symmetry_metal_ion_refined | |
r_symmetry_metal_ion_other | |
r_scangle_it | |
r_rigid_bond_restr | |
r_sphericity_free | |
r_sphericity_bonded | |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 5930 |
Nucleic Acid Atoms | |
Solvent Atoms | 40 |
Heterogen Atoms | 27 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHENIX | phasing |