Plasmodium falciparum lipocalin (PF3D7_0925900)
X-RAY DIFFRACTION - SOLUTION SCATTERING
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 3MBT | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION | 7 | 292 | 0.2 M magnesium chloride, 0.1 M Tris pH7, 2.5 M Sodium Chloride |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.7 | 66.76 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 63.993 | α = 90 |
| b = 92.25 | β = 98.35 |
| c = 214.502 | γ = 90 |
| Symmetry |
|---|
| Space Group | I 1 2 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 | PIXEL | DECTRIS PILATUS 6M | | 2019-03-05 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9762 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
| Overall |
|---|
| 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 |
|---|
| 1 | 2.85 | 56.2 | 99.75 | 0.1985 | | 0.2943 | | 0.546 | | 3.69 | 2 | | 28936 | | | 54.95 |
| Highest Resolution Shell |
|---|
| 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) |
|---|
| 1 | 2.85 | 2.952 | | | | | | 0.41 | | 1.19 | | |
Refinement
| Statistics |
|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.85 | 56.2 | | | | 27535 | 1428 | 99.75 | | 0.1912 | 0.18886 | 0.2 | 0.23647 | 0.24 | RANDOM | 53.494 |
| 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] |
|---|
| -0.09 | | -0.04 | 0.09 | | 0.01 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| 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 |
|---|
| Key | Refinement Restraint Deviation |
|---|
| 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 |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 5930 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 40 |
| Heterogen Atoms | 27 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHENIX | phasing |