2PVB
PIKE PARVALBUMIN (PI 4.10) AT LOW TEMPERATURE (100K) AND ATOMIC RESOLUTION (0.91 A).
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PVB | PDB ENTRY 1PVB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | vapor diffusion - sitting drop in microgravity | 8 | SITTING DROP, MICROGRAVITY CONDITIONS PROTEIN SOLUTION : 27 MG/ML, 0.02% (W/V) NAN3 RESERVOIR : 2.4M AMMONIUM SULFATE 0.03%(W/V) EDTA, 0.02% (W/V) NAN3 TRIS BUFFER (PH 8.0) DROP : 10 MICROL. PROTEIN SOLUTION + 10 MICROL. RESERVOIR, vapor diffusion - sitting drop in microgravity |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.93 | 36.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.03 | α = 90 |
b = 49.81 | β = 90 |
c = 34.57 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | IMAGE PLATE | MARRESEARCH | SEGMENTED MIRROR | 1997-06-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 0.91 | 25 | 99.8 | 3.6 | 14.2 | 4.9 | 63698 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
0.91 | 0.92 | 97.3 | 12.4 | 3.3 | 2.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | OTHER | THROUGHOUT | PDB ENTRY 1PVB | 0.91 | 25 | 63698 | 3187 | 99.8 | 0.1098 | 0.1095 | 0.1317 | RANDOM, 5% |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
16 | 784 | 1025 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.335 |
s_non_zero_chiral_vol | 0.102 |
s_approx_iso_adps | 0.1 |
s_zero_chiral_vol | 0.093 |
s_anti_bump_dis_restr | 0.061 |
s_similar_adp_cmpnt | 0.037 |
s_angle_d | 0.032 |
s_bond_d | 0.015 |
s_rigid_bond_adp_cmpnt | 0.007 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 873 |
Nucleic Acid Atoms | |
Solvent Atoms | 217 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |