3BBF
Crystal structure of the NM23-H2 transcription factor complex with GDP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NUE | pdb entry 1NUE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 283 | PEG 1500, 50 mM Tris-HCl, 200 mM MgCl2, 2 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.75 | α = 90 |
b = 86.78 | β = 90 |
c = 159.12 | 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 | MAR CCD 165 mm | bent Si-mirror | 2004-03-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 1.1271 | APS | 14-ID-B |
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 | 30 | 96.6 | 0.062 | 25.4 | 6.5 | 103223 | 103223 |
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 | 1.76 | 81.4 | 0.33 | 3.3 | 4.3 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 1NUE | 1.7 | 30 | 97878 | 5172 | 96.51 | 0.19811 | 0.19608 | 0.2 | 0.23592 | 0.24 | RANDOM | 15.833 |
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] | |
-0.26 | 0.01 | 0.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.997 |
r_dihedral_angle_4_deg | 22.356 |
r_dihedral_angle_3_deg | 14.619 |
r_dihedral_angle_1_deg | 6.638 |
r_scangle_it | 3.011 |
r_scbond_it | 2.166 |
r_angle_refined_deg | 1.669 |
r_mcangle_it | 1.268 |
r_mcbond_it | 1.068 |
r_angle_other_deg | 1.029 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7260 |
Nucleic Acid Atoms | |
Solvent Atoms | 658 |
Heterogen Atoms | 190 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDISPLAYF | data collection |
CrystalClear | data reduction |
CrystalClear | data scaling |
MOLREP | phasing |