5CSD
Ligand binding domain 2 of Penicillium marneffei MP1 protein in complex with arachidonic acids
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 298 | PEG 4000, Sodium Acetate, Ammonium Acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.502 | α = 90 |
b = 100.052 | β = 90.01 |
c = 99.05 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | ADSC QUANTUM 315r | 2012-03-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.9793 | SSRF | BL17U |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.45 | 50 | 99.2 | 0.087 | 13.8 | 3.9 | 100087 |
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 | 1.45 | 1.5 | 95.8 | 0.303 | 3.1 | 9574 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.45 | 44.99 | 95019 | 4995 | 98.96 | 0.1823 | 0.1812 | 0.2039 | RANDOM | 18.396 |
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] | |
-0.24 | 0.02 | 0.14 | 0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.813 |
r_dihedral_angle_4_deg | 14.742 |
r_dihedral_angle_3_deg | 12.754 |
r_dihedral_angle_1_deg | 3.503 |
r_angle_other_deg | 1.964 |
r_angle_refined_deg | 1.673 |
r_mcangle_it | 1.031 |
r_mcbond_it | 0.639 |
r_mcbond_other | 0.636 |
r_chiral_restr | 0.09 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4741 |
Nucleic Acid Atoms | |
Solvent Atoms | 657 |
Heterogen Atoms | 144 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data collection |
SCALEPACK | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
Coot | model building |
Blu-Ice | data collection |