4AHR
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 | 1BI4 | PDB ENTRY 1BI4 |
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 |
2.9 | 57.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.981 | α = 90 |
b = 70.981 | β = 90 |
c = 66.611 | 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 | 2008-03-14 | 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 | 1.9 | 61.4 | 99.3 | 0.1 | 12.7 | 4.7 | 29399 | 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 | 1.9 | 2 | 95.3 | 0.53 | 2.3 | 3.6 |
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 1BI4 | 1.9 | 66.67 | 27427 | 1458 | 97.64 | 0.19605 | 0.19399 | 0.23441 | RANDOM | 28.535 |
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] | |
0.03 | 0.02 | 0.03 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.372 |
r_dihedral_angle_3_deg | 16.251 |
r_dihedral_angle_4_deg | 14.854 |
r_dihedral_angle_1_deg | 6.586 |
r_angle_refined_deg | 2.04 |
r_chiral_restr | 0.133 |
r_bond_refined_d | 0.02 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2359 |
Nucleic Acid Atoms | |
Solvent Atoms | 126 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |