3CWH
D-xylose Isomerase in complex with linear product, per-deuterated xylulose
NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4XIS | PDB entry 4XIS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 293 | 50MM TRIS-HCL, 38%(NH4)2SO4, 2MM MG2+ XI @ 125 MG/ML, PH=8.0, LIQUID DIFFUSION, T=293K; NATIVE CRYSTAL WERE SOAKED WITH 0.2M PER-DEUTERATED XYLOSE IN D2O BUFFERED IN 50MM TRIS-DCL, PH=7.6 (PD=8.0), 2MM MGCL2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.64 | α = 90 |
b = 99.97 | β = 90 |
c = 103.97 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 | neutron | 293 | AREA DETECTOR | TIME-OF-FLIGHT MULTIWIRE HE3 NE | 2004-09-01 | L | LAUE |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | NUCLEAR REACTOR | PCS |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.2 | 100 | 89.4 | 0.25 | 5.8 | 5.4 | 21892 | 1.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.32 | 81.3 | 0.38 | 2 | 3.3 |
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 (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | FREE R | PDB entry 4XIS | 2.2 | 20 | 17072 | 876 | 86.3 | 0.237 | 0.288 | RANDOM | 20.7 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_angle_d | 0.962 |
s_bond_d | 0.007 |
s_similar_dist | |
s_from_restr_planes | |
s_zero_chiral_vol | |
s_non_zero_chiral_vol | |
s_anti_bump_dis_restr | |
s_rigid_bond_adp_cmpnt | |
s_similar_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3046 |
Nucleic Acid Atoms | |
Solvent Atoms | 227 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
SHELXL-97 | refinement |
d*TREK | data reduction |
LAUENORM | data scaling |
CNS | phasing |