Human carbonmonoxy hemoglobin SFX dataset
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 2DN2 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 7 | 293 | batch crystallization, using 1.6 M Na/K phosphate, neutal pH as precipitant |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.3 | 46.45 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 55.8 | α = 90 |
| b = 157.4 | β = 90 |
| c = 64.2 | 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 | MPCCD | KB mirror | 2017-12-09 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.7 | SACLA | BL2 |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.2 | 39.35 | 99.9 | 0.98 | 0.115 | 6.5 | 1 | | 29516 | | | 42.37 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 2.2 | 2.26 | 100 | | 0.654 | 0.466 | | 1 | |
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 | FOURIER SYNTHESIS | FREE R-VALUE | 2DN2 | 2.2 | 39.35 | 29515 | 1542 | 99.96 | 0.184 | 0.1825 | 0.2 | 0.2113 | 0.22 | RANDOM | 43.54 |
| 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] |
|---|
| 3.637 | | | -0.6404 | | -2.9966 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| t_other_torsion | 19.09 |
| t_omega_torsion | 2.18 |
| t_angle_deg | 0.98 |
| t_bond_d | 0.01 |
| t_dihedral_angle_d | |
| t_incorr_chiral_ct | |
| t_pseud_angle | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| t_other_torsion | 19.09 |
| t_omega_torsion | 2.18 |
| t_angle_deg | 0.98 |
| t_bond_d | 0.01 |
| t_dihedral_angle_d | |
| t_incorr_chiral_ct | |
| t_pseud_angle | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| t_nbd | |
| t_improper_torsion | |
| t_chiral_improper_torsion | |
| t_sum_occupancies | |
| t_utility_distance | |
| t_utility_angle | |
| t_utility_torsion | |
| t_ideal_dist_contact | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 4332 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 20 |
| Heterogen Atoms | 180 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PDB_EXTRACT | data extraction |
| CrystFEL | data reduction |
| XSCALE | data scaling |
| Coot | model building |
| REFMAC | phasing |
| BUSTER | refinement |
