4MU4
The form B structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and its substrate, 2R3S-IGP, to 1.41 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2F1D | PDB ENTRY 2F1D |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 290 | 0.05% PEG2000, 0.4 M succinic acid, pH 7.0, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.68 | 54.07 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 112.9 | α = 90 |
b = 112.9 | β = 90 |
c = 112.9 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 4 3 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | two K-B pairs of bimorph type mirrors | 2011-11-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9686 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.41 | 65.183 | 100 | 0.085 | 17.7 | 10.5 | 47547 | 47547 | 12.197 |
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 | 1.41 | 1.45 | 100 | 0.849 | 3.4 | 10.8 | 3450 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2F1D | 1.41 | 65.183 | 47547 | 45244 | 2303 | 99.93 | 0.12495 | 0.12347 | 0.1536 | RANDOM | 17.769 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
r_sphericity_free | 35.447 |
r_sphericity_bonded | 32.863 |
r_dihedral_angle_2_deg | 31.967 |
r_dihedral_angle_4_deg | 14.888 |
r_rigid_bond_restr | 12.77 |
r_dihedral_angle_3_deg | 10.984 |
r_scbond_it | 7.915 |
r_scbond_other | 7.91 |
r_scangle_other | 7.09 |
r_long_range_B_other | 6.838 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1533 |
Nucleic Acid Atoms | |
Solvent Atoms | 196 |
Heterogen Atoms | 29 |
Software
Software | |
---|---|
Software Name | Purpose |
GDA | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
SCALA | data scaling |