8VW1
Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ADP bound)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 8V8Y |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2, 2% (v/v) DMSO. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. 4 hour soak in 5 mM ADP. plate 13768 well E4 drop 1 or 2. Puck: PSL-1105, Cryo: direct |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.12 | 42 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 58.47 | α = 90 |
b = 69.235 | β = 90 |
c = 100.468 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 EIGER2 XE 9M | 2023-12-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.9785 | NSLS-II | 19-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.7 | 44.67 | 99.9 | 0.096 | 0.1 | 0.028 | 0.999 | 15 | 13.2 | 45584 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.7 | 1.73 | 99.4 | 1.874 | 1.945 | 0.519 | 0.723 | 13.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.7 | 40.82 | 1.34 | 45480 | 2238 | 99.73 | 0.1644 | 0.1628 | 0.1967 |
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 |
f_dihedral_angle_d | 13.976 |
f_angle_d | 1.047 |
f_chiral_restr | 0.059 |
f_bond_d | 0.009 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3252 |
Nucleic Acid Atoms | |
Solvent Atoms | 220 |
Heterogen Atoms | 45 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |