3PMB
2.9 Angstrom crystal structure of bovine thrombin in tetragonal spacegroup
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 295 | 3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v PEG3350, 15% v/v 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.81 | 56.2 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 87.644 | α = 90 |
b = 87.644 | β = 90 |
c = 194.514 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 104 | IMAGE PLATE | RIGAKU RAXIS IV++ | Rigaku Varimax Confocal Optics | 2008-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 |
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 | 2.8 | 39.2 | 85.9 | 0.167 | 6.9 | 4.19 | 19432 | 16696 |
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 | 2.8 | 2.9 | 97.7 | 0.335 | 4.3 | 4.62 | 1887 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.9 | 15 | 17545 | 14714 | 746 | 84.6 | 0.24499 | 0.24201 | 0.30068 | RANDOM | 35.286 |
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] | |
-1.07 | -1.07 | 2.15 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.331 |
r_dihedral_angle_4_deg | 19.952 |
r_dihedral_angle_3_deg | 19.733 |
r_dihedral_angle_1_deg | 4.831 |
r_angle_refined_deg | 1.23 |
r_scangle_it | 0.891 |
r_scbond_it | 0.504 |
r_mcangle_it | 0.459 |
r_mcbond_it | 0.246 |
r_chiral_restr | 0.077 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4255 |
Nucleic Acid Atoms | |
Solvent Atoms | 74 |
Heterogen Atoms | 2 |
Software
Software | |
---|---|
Software Name | Purpose |
CrystalClear | data collection |
PHENIX | model building |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
PHENIX | phasing |