4AHT
Parallel screening of a low molecular weight compound library: do differences in methodology affect hit identification
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4AHR | PDB ENTRY 4AHR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | PROTEIN: 5.5MG/ML IN 40MM TRIS BUFFER AT PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT. CRYSTALLANT: 100MM SODIUM ACETATE PH 5.0 TO 5.5, 1.2 TO 1.5M AMMONIUM SULFATE AT 20C IN SITTING DROP PLATES. FRAGMENTS WERE SOAKED INTO PREFORMED CRYSTALS 24-48 HOURS PRIOR TO DATA COLLECTION. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.742 | α = 90 |
b = 70.742 | β = 90 |
c = 66.608 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 210r | 2008-04-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | Australian Synchrotron | MX1 |
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 | 1.8 | 61.3 | 94.7 | 0.07 | 16.6 | 5.3 | 32746 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.8 | 1.9 | 73.4 | 0.5 | 2.4 | 3.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB ENTRY 4AHR | 1.8 | 61.31 | 31075 | 1643 | 94.74 | 0.16173 | 0.15978 | 0.1982 | RANDOM | 23.138 |
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] | |
0.11 | 0.06 | 0.11 | -0.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.981 |
r_dihedral_angle_4_deg | 20.643 |
r_dihedral_angle_3_deg | 16.129 |
r_dihedral_angle_1_deg | 6.449 |
r_angle_refined_deg | 2.428 |
r_chiral_restr | 0.173 |
r_bond_refined_d | 0.024 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2334 |
Nucleic Acid Atoms | |
Solvent Atoms | 178 |
Heterogen Atoms | 102 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |