5NXB
Mouse galactocerebrosidase in complex with saposin A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 293 | 800 nL of protein (90 uM GALC plus 180 uM SapA) was mixed with 800 nL of reservoir solution (75 mM Sodium citrate pH 5.6, 11% PEG 3350) and equilibrated against 200 uL reservoirs at 20C. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.41 | 77.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 187.183 | α = 90 |
b = 187.183 | β = 90 |
c = 360.24 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 2 |
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 PILATUS 6M-F | Toroidal mirrors | 2015-07-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92818 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 3.6 | 180.12 | 100 | 0.386 | 0.945 | 9.3 | 25.6 | 44024 | 61.93 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.6 | 3.7 | 100 | 2.946 | 0.677 | 25.2 |
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 | 4CCE, 4DDJ | 3.6 | 162.11 | 43825 | 2138 | 99.7 | 0.218 | 0.217 | 0.231 | RANDOM | 101.63 |
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] | |
-0.463 | -0.463 | 0.9261 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.39 |
t_omega_torsion | 3.38 |
t_angle_deg | 0.94 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11522 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 220 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |