4MJ2
Crystal structure of apo-iduronidase in the R3 form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 0.01 M HEPES, pH 7.5, 0.26 M sodium potassium tartrate, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 297K, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 259.36 | α = 90 |
b = 259.36 | β = 90 |
c = 71.81 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | RAYONIX MX300HE | collimating mirror with two stripes (Si, Rh/Pt) and toroidal focusing mirror (Rh/Pt) | 2013-02-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08B1-1 | 0.9793 | CLSI | 08B1-1 |
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 | 2.1 | 49.01 | 99.54 | 0.139 | 12.22 | 10.7 | 104643 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.154 | 95.32 | 0.868 | 2.33 | 6.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 2.1 | 49.01 | 99410 | 5233 | 99.54 | 0.19215 | 0.19215 | 0.1914 | 0.20637 | RANDOM | 36.056 |
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] | |
-1.84 | -1.84 | -1.84 | 5.97 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.145 |
r_dihedral_angle_4_deg | 15.497 |
r_dihedral_angle_3_deg | 12.433 |
r_dihedral_angle_1_deg | 5.767 |
r_angle_refined_deg | 1.006 |
r_angle_other_deg | 0.708 |
r_chiral_restr | 0.057 |
r_bond_refined_d | 0.005 |
r_gen_planes_refined | 0.003 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9551 |
Nucleic Acid Atoms | |
Solvent Atoms | 433 |
Heterogen Atoms | 307 |
Software
Software | |
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Software Name | Purpose |
MxDC | data collection |
PHENIX | model building |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |