3V7M
Crystal structure of monoclonal human anti-Rhesus D Fc IgG1 T125(YB2/0) in the presence of Zn2+
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2J6E | 2J6E FC PORTION ONLY. |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.1 | 316 | 8% MPEG 5000, 300 MICRO-M ZNCL2, 100 MICRO-M NICL2, 0.1 M SODIUM CACODYLATE, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 316KK |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.96 | 58.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.22 | α = 90 |
b = 147.75 | β = 90 |
c = 75.54 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | ADSC QUANTUM 4 | MIRRORS | 2003-06-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.02 | 45 | 93.2 | 0.063 | 0.059 | 18.81 | 7.2 | 17681 | -2 | 47.34 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.02 | 2.14 | 70.1 | 0.759 | 0.712 | 2.71 | 6.62 |
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 | 2J6E FC PORTION ONLY. | 2.02 | 40.24 | 16796 | 884 | 100 | 0.237 | 0.234 | 0.286 | RANDOM | 47.93 |
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] | |
-1.13 | -0.45 | 1.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.152 |
r_dihedral_angle_3_deg | 22.107 |
r_dihedral_angle_4_deg | 20.147 |
r_dihedral_angle_1_deg | 7.136 |
r_scangle_it | 4.963 |
r_scbond_it | 3.185 |
r_mcangle_it | 2.576 |
r_angle_refined_deg | 2.136 |
r_mcbond_it | 1.465 |
r_chiral_restr | 0.154 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1669 |
Nucleic Acid Atoms | |
Solvent Atoms | 142 |
Heterogen Atoms | 124 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |