Neutron and X-ray structure analysis of xylanase: N44D at pH6
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1RX2 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 291 | 16% PEG8000, 0.2 M NaI, 0.1 M HEPES at pH 7.0 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.52 | 51.24 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 49.194 | α = 90 |
| b = 60.287 | β = 90 |
| c = 70.52 | 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 | 290 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2013-03-27 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 290 | AREA DETECTOR | CUSTOM-MADE | | 2013-03-12 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
| 2 | NUCLEAR REACTOR | LANSCE BEAMLINE PCS | 0.7-6.0 | LANSCE | PCS |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 50 | 96.2 | 0.071 | | | | | | 13.4 | 4 | | 22851 | | | |
| 2 | 2 | 22.85 | 85.5 | 0.223 | | | | | | 5 | 3.3 | | 12398 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.7 | 1.76 | 99.6 | 0.468 | | | | | | | 3.8 | |
| 2 | 2 | 2.11 | 72.7 | 0.369 | | | | | | | 2 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.7 | 20 | | | | 22806 | | 96 | | | 0.133 | 0.13 | 0.157 | 0.16 | RANDOM | 18.41 |
| NEUTRON DIFFRACTION | | 2 | 20 | | | | | | 80.3 | | | 0.264 | | 0.304 | | RANDOM | |
| 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 | 9.649 |
| f_angle_d | 1.213 |
| f_chiral_restr | 0.095 |
| f_bond_d | 0.014 |
| f_plane_restr | 0.007 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1472 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 519 |
| Heterogen Atoms | 3 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| SCALEPACK | data reduction |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| SCALEPACK | data scaling |
| PHASER | phasing |
