4BJH
Crystal Structure of the Aquifex Reactor Complex Formed by Dihydroorotase (H180A, H232A) with Dihydroorotate and Aspartate Transcarbamoylase with N-(phosphonacetyl)-L-aspartate (PALA)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3D6N | PDB ENTRY 3D6N |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | THE CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN HANGING-DROPS. THE HETERO DODECAMER WAS BUFFER EXCHANGED INTO 10 MM HEPES, 1 MM TCEP PH 7.5, AT A FINAL PROTEIN CONCENTRATION OF 3.0 MG/ML. DHO-ATC SOLUTION (3-6 UL) WAS MIXED WITH 1 UL OF RESERVOIR SOLUTION (30% ETHYLENE GLYCOL) FOLLOWED BY 10% OF THE DROP VOLUME (V/V) OF 100 MM BARIUM CHLORIDE. THE FINAL CRYSTALLIZATION PH WAS 6.3. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.17 | 61.2 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 157.152 | α = 90 |
b = 157.152 | β = 90 |
c = 233.244 | γ = 120 |
Symmetry | |
---|---|
Space Group | H 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 | CCD | MARRESEARCH MAR300 | BE LENSES | 2009-05-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | APS | 21-ID-G |
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 | 2.2 | 77.85 | 99.9 | 0.1 | 16.2 | 8.8 | 53365 | 41.7 |
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 | 2.2 | 2.32 | 100 | 0.76 | 2.3 | 8.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PDB ENTRY 3D6N | 2.2 | 77.85 | 53365 | 2846 | 99.94 | 0.16282 | 0.16066 | 0.20304 | RANDOM | 41.256 |
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] | |
-0.27 | -0.14 | -0.27 | 0.41 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.837 |
r_dihedral_angle_4_deg | 23.094 |
r_dihedral_angle_3_deg | 15.736 |
r_dihedral_angle_1_deg | 6.491 |
r_scangle_it | 4.184 |
r_scbond_it | 2.588 |
r_angle_refined_deg | 1.558 |
r_mcangle_it | 1.423 |
r_mcbond_it | 0.738 |
r_chiral_restr | 0.104 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5622 |
Nucleic Acid Atoms | |
Solvent Atoms | 445 |
Heterogen Atoms | 84 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALEPACK | data scaling |
ARP/wARP | phasing |