3MVN
Crystal structure of a domain from a putative UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-medo-diaminopimelate ligase from Haemophilus ducreyi 35000HP
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 294 | 2 M Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.61 | 23.69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 46.996 | α = 90 |
| b = 46.996 | β = 90 |
| c = 106.628 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 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 | MIRROR | 2010-04-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97872 | APS | 21-ID-G |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.9 | 20.62 | 99.2 | 0.08 | 0.08 | 40.489 | 13.7 | 10007 | 10007 | -3 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1.9 | 1.93 | 100 | 0.446 | 0.446 | 7.1 | 14.4 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.9 | 20.62 | 9943 | 9464 | 479 | 99.21 | 0.1622 | 0.1588 | 0.23707 | RANDOM | 23.008 | ||||||
| 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_dihedral_angle_2_deg | 44.096 |
| r_dihedral_angle_4_deg | 15.132 |
| r_dihedral_angle_3_deg | 14.194 |
| r_scangle_it | 5.915 |
| r_dihedral_angle_1_deg | 5.707 |
| r_scbond_it | 3.812 |
| r_mcangle_it | 2.313 |
| r_rigid_bond_restr | 1.766 |
| r_mcbond_it | 1.45 |
| r_angle_refined_deg | 1.412 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 950 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 67 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Blu-Ice | data collection |
| HKL-3000 | phasing |
| MLPHARE | phasing |
| DM | model building |
| SHELXD | phasing |
| ARP/wARP | model building |
| Coot | model building |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| DM | phasing |
