6W04
Crystal structure of HAD hydrolase, family IA, variant 3 from Entamoeba histolytica HM-1:IMSS
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 290 | 24.5 mg/mL EnhiA.01283.a.AE1.PS38608 (labeled as BrabA.17285.c.AE2) in 3 mM magnesium chloride against MCSG1_A2-C2 optimization screen, condition g3 (200 mM ammonium sulfate, 26% w/v PEG3350, 100 mM Bis-Tris-HCl, pH 5.4), cryoprotectant: 15% ethylene glycol + 3 mM magnesium chloride in two steps, tray: 314701g3, puck wrw2-2, for experimental phasing, a crystal from MCSG1_A2-C2 optimization screen, condition e7 (300 mM lithium sulfate, 24% w/v PEG3350, 100 mM Bis-Tris-HCl, pH 5.0) was soaked for 20 seconds in 90% reservoir + 10% 5 M sodium iodide in ethylene glycol, followed by another 20-second soak in 80% reservoir + 20% 5 M sodium iodide in ethylene glycol, vitrified in liquid nitrogen, tray 314703e7, puck ynn3-8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.91 | α = 90 |
b = 100.91 | β = 90 |
c = 45.24 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX-300 | 2020-02-05 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2020-02-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.95 | 50 | 100 | 0.063 | 0.068 | 0.998 | 18.53 | 7.521 | 19394 | 40.227 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.95 | 2 | 100 | 0.494 | 0.53 | 0.9 | 3.8 | 7.568 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | FREE R-VALUE | 1.95 | 33.03 | 1.37 | 19390 | 1876 | 99.97 | 0.1629 | 0.1579 | 0.2107 | 0 | 42.11 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.0766 |
f_angle_d | 0.8897 |
f_chiral_restr | 0.0575 |
f_bond_d | 0.0089 |
f_plane_restr | 0.0051 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1763 |
Nucleic Acid Atoms | |
Solvent Atoms | 151 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
ARP/wARP | model building |
Coot | model building |