6GJT
Chlamydia protein Pgp3 studied at high resolution in a new crystal form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | A 7mg per ml Pgp3 stock buffered with 220mM NaCl, 50mM Tris-HCl pH 7.5 and 5mM DTT was screened for suitable crystallization conditions in sitting drop vapour diffusion format using a Mosquito robot (TTP Labtech, UK). A variety of commercially available screens such as Crystal Screen HT, Index HT (Hampton Research, USA), Morpheus and PGA (Molecular Dimensions, UK) were used in 96 well MRC crystallization plates (Molecular Dimensions, UK). All screening trials contained 400 nanolitre drops, each mixed in a 1 to 1 ratio of the protein and the screen solutions. The crystallization trials were incubated at 293K. The different leads obtained from the crystallization screening trials were optimised by determining working phase diagrams as detailed in Saridakis and Chayen (Saridakis & Chayen 2000). Each optimisation trial was also scaled up to 1 microlitre drop volume and set up manually in hanging drops (Qiagen Nextal plates) and in microbatch experiments (Chayen 1999). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.41 | α = 90 |
b = 108.25 | β = 90 |
c = 207 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | PIXEL | DECTRIS PILATUS3 S 6M | 2012-04-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9173 | Diamond | I04 |
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 | 1.98 | 45.7 | 98.1 | 0.2 | 9.7 | 11.7 | 130981 | 26.9 |
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 | 1.98 | 2 | 98.3 | 1.875 | 1.8 |
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 | 4JDM | 1.98 | 42.62 | 124208 | 6594 | 97.77 | 0.27407 | 0.2731 | 0.2922 | RANDOM | 36.304 |
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 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.866 |
r_dihedral_angle_4_deg | 17.051 |
r_dihedral_angle_3_deg | 15.091 |
r_long_range_B_refined | 8.798 |
r_long_range_B_other | 8.798 |
r_dihedral_angle_1_deg | 6.764 |
r_scangle_other | 6.227 |
r_mcangle_other | 5.132 |
r_mcangle_it | 5.13 |
r_scbond_it | 4.29 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7950 |
Nucleic Acid Atoms | |
Solvent Atoms | 156 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |