5JOM
X-ray structure of CO-bound sperm whale myoglobin using a fixed target crystallography chip
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1VXA |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 9 | 293 | 10 mM Tris-HCl, pH 9.0, 2.2-2.5 M ammonium sulfate |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.18 | 43.5 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 38.13 | α = 90 |
b = 46.483 | β = 90 |
c = 84.521 | 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 | 293 | CCD | RAYONIX MX170-HS | 2015-03-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE XPP | 1.293 | SLAC LCLS | XPP |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.9 | 33.43 | 100 | 0.996 | 6 | 51.6 | 12354 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.9 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1VXA | 1.9 | 33.43 | 11780 | 602 | 99.97 | 0.21402 | 0.21169 | 0.22 | 0.259 | 0.26 | RANDOM | 39.726 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.66 | -0.34 | -0.32 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.573 |
r_dihedral_angle_4_deg | 24.083 |
r_dihedral_angle_3_deg | 16.599 |
r_long_range_B_refined | 7.436 |
r_long_range_B_other | 7.434 |
r_scangle_other | 6.597 |
r_dihedral_angle_1_deg | 5.684 |
r_scbond_it | 4.299 |
r_scbond_other | 4.284 |
r_mcangle_it | 3.753 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1225 |
Nucleic Acid Atoms | |
Solvent Atoms | 20 |
Heterogen Atoms | 50 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
Cheetah | data collection |
DIALS | data scaling |
CPPXFEL | data processing |
CPPXFEL | data reduction |
CPPXFEL | data scaling |
PHASER | phasing |