3W6P
Crystal structure of human Dlp1 in complex with GDP.AlF4
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3W6N |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 20% PEG 550 MME, 0.05M calcium chloride, 0.1M Bis-Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.76 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 51.41 | ¦Á = 90 |
b = 109.13 | ¦Â = 90 |
c = 128.73 | ¦Ã = 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 | MARMOSAIC 225 mm CCD | mirrors | 2010-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.0000 | SLS | X06DA |
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 | 50 | 98.7 | 0.061 | 20.1 | 4.8 | 80512 | 79457 |
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 | 1.7 | 1.74 | 97.7 | 0.361 | 4.4 | 4.6 | 5874 |
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 | 3W6N | 1.7 | 30 | 75441 | 4006 | 98.71 | 0.18383 | 0.18222 | 0.18 | 0.21412 | 0.21 | RANDOM | 18.17 |
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] | |
-0.14 | -0.15 | 0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.827 |
r_dihedral_angle_4_deg | 17.358 |
r_dihedral_angle_3_deg | 13.152 |
r_dihedral_angle_1_deg | 4.929 |
r_scangle_it | 3.112 |
r_scbond_it | 1.845 |
r_angle_refined_deg | 1.215 |
r_mcangle_it | 1.176 |
r_mcbond_it | 0.625 |
r_chiral_restr | 0.079 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5289 |
Nucleic Acid Atoms | |
Solvent Atoms | 704 |
Heterogen Atoms | 97 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |