3M1X
Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica, rhomobohedral form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XRG | PDB entry 1XRG modified with CCP4 program CHAINSAW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 3.5 | 290 | INDEX SCREEN CONDITION D4: 100MM CITRATE, 25% PEG 3350, ENHIA.00579.A AT 25.8 MG/ML, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.69 | 27.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.546 | α = 90 |
b = 78.546 | β = 90 |
c = 89.18 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
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 | 2010-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | SSRL | BL7-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.2 | 54.09 | 99.1 | 0.047 | 6 | 32783 | 32477 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.2 | 1.27 | 94 | 5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1XRG modified with CCP4 program CHAINSAW | 1.2 | 54.085 | 32783 | 32453 | 1647 | 0.107 | 0.107 | 0.106 | 0.131 | RANDOM | 8.16 |
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] | |
0.01 | 0.01 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.862 |
r_dihedral_angle_3_deg | 10.133 |
r_dihedral_angle_4_deg | 9.22 |
r_scangle_it | 6.511 |
r_dihedral_angle_1_deg | 6.507 |
r_scbond_it | 4.537 |
r_mcbond_other | 2.965 |
r_mcangle_it | 2.909 |
r_rigid_bond_restr | 2.42 |
r_angle_refined_deg | 2.206 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 919 |
Nucleic Acid Atoms | |
Solvent Atoms | 171 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |