4ZZ4
Neutron crystal structure of ribonuclease A determined by the real space D/H contrast method
NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1KF5 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | LIQUID DIFFUSION | 293 | a H2O-solvent crystal was sealed in a capillary with D2O-buffer containing 20 mg/mL ribonuclease A, 0.05 M sodium acetate, and 50% 2-d8-propanol (pD 5.8) to exchange hydrogen atoms in the crystal with deuterium atoms. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.17 | 43.41 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 30.34 | α = 90 |
b = 38.369 | β = 105.75 |
c = 53.188 | 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 | neutron | 293 | IMAGE PLATE | MACSCIENCE | The BIX-3 neutron diffractometer at JRR-3M of JAEA | 2009-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | NUCLEAR REACTOR | JRR-3M BEAMLINE 1G-A | 2.9 | JRR-3M | 1G-A |
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 | 1.798 | 100 | 72.1 | 0.114 | 7.3 | 1.8 | 7960 | 14.96 |
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 | 1.798 | 1.86 | 51.3 | 0.344 | 1.4 | 562 |
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 | ||||||
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1KF5 | 1.798 | 51.19 | 7953 | 801 | 71.56 | 0.1991 | 0.1967 | 0.2205 | Random selection | 22.3728 |
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 | 16.486 |
f_angle_d | 0.98 |
f_chiral_restr | 0.054 |
f_bond_d | 0.01 |
f_plane_restr | 0.005 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data scaling |
AMoRE | phasing |
Coot | model building |
PDB_EXTRACT | data extraction |
DENZO | data reduction |