2ZKM
Crystal Structure of Phospholipase C Beta 2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2FJU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 291 | 16%(v/v) isopropanol, 2%(v/v) dioxane, 100mM Tris , pH 8.5, VAPOR DIFFUSION, sitting drop, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.404 | α = 90 |
b = 86.379 | β = 90 |
c = 147.447 | 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 | MARMOSAIC 300 mm CCD | 2004-10-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0712 | APS | 22-ID |
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 | 1.62 | 50 | 98.6 | 0.065 | 12.2 | 4.6 | 130702 | 129374 |
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) | |||||||||||
1.62 | 1.68 | 95.3 | 0.207 | 3.5 | 12374 |
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 (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 | 2FJU | 1.62 | 19.45 | 130702 | 129234 | 6470 | 98.88 | 0.197 | 0.196 | 0.213 | RANDOM | 16.682 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.289 |
r_dihedral_angle_3_deg | 11.155 |
r_dihedral_angle_4_deg | 9.915 |
r_dihedral_angle_1_deg | 5.611 |
r_scangle_it | 1.986 |
r_scbond_it | 1.295 |
r_angle_refined_deg | 0.991 |
r_mcangle_it | 0.845 |
r_mcbond_it | 0.509 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5704 |
Nucleic Acid Atoms | |
Solvent Atoms | 692 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |