A Joint Neutron and X-ray structure of Oxidized Amicyanin
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | | | 291 | 2.4M ammonium sulfate, 100mM citric acid pH5 and 3M sodium monobasic/potassium dibasic phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 1.94 | 36.76 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 27.54 | α = 90 |
| b = 56.58 | β = 96.21 |
| c = 28.86 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 1 21 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | CCD | ADSC QUANTUM 315 | MIRRORS | | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | TOF AREA DETECTOR | IMAGE PLATE | | | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.98 | APS | 24-ID-C |
| 2 | NUCLEAR REACTOR | LANSCE BEAMLINE PCS | 1.1-5 | 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 | 1.8 | 28 | | 0.256 | | | | | | 4.2 | 3.4 | | | | | |
| 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 | 1.8 | 1.85 | | 0.41 | | | | | | 1.5 | 2.3 | 1635 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B |
|---|
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.8 | 28 | | | | 6078 | | | | 0.209 | 0.209 | 0.234 | RANDOM | |
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.5 | 50 | | | | 11364 | | 95.4 | | | 0.198 | 0.215 | | |
| 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 |
|---|
| c_dihedral_angle_d | 17.6 |
| c_angle_deg | 2 |
| c_improper_angle_d | 1.65 |
| c_bond_d | 0.021 |
| c_bond_d_na | |
| c_bond_d_prot | |
| c_angle_d | |
| c_angle_d_na | |
| c_angle_d_prot | |
| c_angle_deg_na | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| c_dihedral_angle_d | 17.6 |
| c_angle_deg | 2 |
| c_improper_angle_d | 1.65 |
| c_bond_d | 0.021 |
| c_bond_d_na | |
| c_bond_d_prot | |
| c_angle_d | |
| c_angle_d_na | |
| c_angle_d_prot | |
| c_angle_deg_na | |
| c_angle_deg_prot | |
| c_dihedral_angle_d_na | |
| c_dihedral_angle_d_prot | |
| c_improper_angle_d_na | |
| c_improper_angle_d_prot | |
| c_mcbond_it | |
| c_mcangle_it | |
| c_scbond_it | |
| c_scangle_it | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 807 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 91 |
| Heterogen Atoms | 1 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| HKL-2000 | data reduction |
| d*TREK | data reduction |
| HKL-2000 | data scaling |
| LAUENORM | data scaling |
| SCALA | data scaling |
| EPMR | phasing |
