3KX6
Crystal structure of fructose-1,6-bisphosphate aldolase from Babesia bovis at 2.1A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PC4 | pdb entry 2PC4 modified with CCP4 program CHAINSAW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 290 | EBS CRYO SCREEN H12: 50% PEG 200, 100MM PHOSPHATE/CITRATE PH 4.2, 200MM NACL; BABOA.00974.A AT 30MG/ML, PH N/A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.52 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 85.88 | ¦Á = 90 |
b = 114.16 | ¦Â = 90 |
c = 174.54 | ¦Ã = 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 | CCD | ADSC QUANTUM 315r | 2009-10-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.3 | 0.975484 | ALS | 5.0.3 |
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 | 20 | 99.2 | 0.071 | 19.7 | 8 | 100767 | 99984 | -3 | 33.47 |
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 | 2.15 | 100 | 0.388 | 5.1 | 8.3 | 7365 |
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 2PC4 modified with CCP4 program CHAINSAW | 2.1 | 20 | 100767 | 99909 | 4992 | 99.4 | 0.162 | 0.162 | 0.16 | 0.193 | RANDOM | 16.18 |
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] | |
0.42 | 1.74 | -2.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.232 |
r_dihedral_angle_4_deg | 19.12 |
r_dihedral_angle_3_deg | 13.399 |
r_dihedral_angle_1_deg | 5.696 |
r_scangle_it | 3.781 |
r_scbond_it | 2.288 |
r_angle_refined_deg | 1.425 |
r_mcangle_it | 1.293 |
r_angle_other_deg | 0.949 |
r_mcbond_it | 0.696 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10279 |
Nucleic Acid Atoms | |
Solvent Atoms | 805 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
BOS | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |