4HVT
Structure of a Post-proline cleaving enzyme from Rickettsia typhi
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 290 | Microlyic MCSG1 screen b10: 24% PEG 4000, 20% Glycerol, 160mM Magnesium Chloride, 80mM Tris:HCl pH 8.5; RityA17583bB2.PS01616 at 26.6mg/ml, cryo: EG; SG C2; for phasing crystal 2 was used SG P21, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
2 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Microlyic MCSG1 screen c5: 20% PEG 3350, 200mM Magnesium acetate; RityA17583bB2.PS01616 at 26.6mg/ml, for phasing a crystal was soaked in reservoir + 20% EG with 2.5M sodium iodide (final 500mM NaI) for 1 minute, this sample is from a differet space group (P21) than crystal 1, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 50 |
2.28 | 46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 199.59 | α = 90 |
b = 73.28 | β = 98.52 |
c = 55.46 | 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 | 2012-10-14 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2012-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.9774 | ALS | 5.0.1 |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | ||||||||
1,2 | 1.7 | 50 | 99 | 0.065 | 16.86 | 4.8 | 87031 | 86126 | -3 | 23.221 |
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) | |||||||||||
1,2 | 1.7 | 1.74 | 98 | 0.493 | 3.42 |
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 | SAD, MOLECULAR REPLACEMENT | THROUGHOUT | An initial model was obtained from iodide SAD phasing using crystal 2 (P21). The initial model was then used as search model for C2 high resolution data set, crystal 1. | 1.7 | 50 | 87031 | 81804 | 4322 | 98.97 | 0.1723 | 0.1723 | 0.1704 | 0.2093 | RANDOM | 19.2341 |
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] | |
0.14 | 0.54 | 0.79 | -0.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.673 |
r_dihedral_angle_3_deg | 12.879 |
r_dihedral_angle_4_deg | 11.997 |
r_dihedral_angle_1_deg | 6.687 |
r_angle_refined_deg | 1.683 |
r_angle_other_deg | 0.85 |
r_chiral_restr | 0.104 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5510 |
Nucleic Acid Atoms | |
Solvent Atoms | 746 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
JDirector | data collection |
XDS | data reduction |