2QU1
Crystal Structure of a Cyclized GFP Variant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | Protein solution (4.95 mg/ml Protein, 0.050 M Sodium chloride, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (0.080 M Calcium chloride, 15% PEG 4000, 0.1 M HEPPS pH 8.5) and cryoprotected with well solution supplemented with 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 42.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.46 | α = 90 |
b = 61.99 | β = 90 |
c = 70.02 | 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 | CCD | BRUKER PROTEUM-R | MONTEL OPTICS | 2007-04-01 | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.7 | 70.2 | 99 | 0.0976 | 28.27 | 29.45 | 25086 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1.7 | 1.75 | 96.8 | 0.6834 | 2.93 | 5.42 | 2000 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2G6E | 1.7 | 46.424 | 25028 | 1276 | 98.98 | 0.171 | 0.168 | 0.22 | RANDOM | 12.341 |
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] | |
0.312 | -0.42 | 0.108 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.293 |
r_dihedral_angle_3_deg | 12.058 |
r_dihedral_angle_4_deg | 11.385 |
r_dihedral_angle_1_deg | 6.337 |
r_scangle_it | 3.52 |
r_scbond_it | 2.291 |
r_angle_refined_deg | 1.548 |
r_mcangle_it | 1.285 |
r_mcbond_it | 0.866 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1915 |
Nucleic Acid Atoms | |
Solvent Atoms | 377 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
SAINT | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PROTEUM PLUS | data collection |
SAINT | data reduction |
SADABS | data scaling |