8ADX
Structure of the Reconstructed Ancestor of Phenolic Acid Decarboxylase AncPAD55
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 289 | Protein in 10mM MES, 150mM NaCl, pH6 INDEX Screen add1: Prot 9 mg/ml add2: Prot 6,75 mg/ml add3: Prot 4,5 mg/ml all drops 1 microliter drop1: 0.5 add1 + 0.5 screen Chrystal: INDEX Screen Condition 5 0.1 M HEPES pH 7.5 & 2.0 Ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.737 | α = 90 |
b = 104.847 | β = 109.865 |
c = 81.495 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 4M | 2021-11-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.967700 | ESRF | MASSIF-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.6 | 43.27 | 96.6 | 0.059 | 0.081 | 0.055 | 0.992 | 10.6 | 3.5 | 116814 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.6 | 1.62 | 0.347 | 0.466 | 0.309 | 0.856 | 3.5 |
Refinement
Statistics | |||||||||||||||||||
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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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4ALB | 1.6 | 43.27 | 116559 | 5831 | 97.145 | 0.19 | 0.188 | 0.2354 | 17.626 |
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] | |
0.265 | 0.57 | -0.629 | -0.038 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 16.423 |
r_dihedral_angle_3_deg | 12.564 |
r_dihedral_angle_2_deg | 9.626 |
r_dihedral_angle_1_deg | 7.448 |
r_rigid_bond_restr | 5.886 |
r_lrange_it | 3.856 |
r_lrange_other | 3.417 |
r_scangle_it | 2.715 |
r_scangle_other | 2.704 |
r_mcangle_other | 2.205 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5452 |
Nucleic Acid Atoms | |
Solvent Atoms | 730 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
PHENIX | model building |
AutoProcess | data reduction |
AutoProcess | data scaling |
PHENIX | phasing |