4BH7
CRYSTAL STRUCTURE OF GERMLINE ANTIBODY 36-65 IN COMPLEX WITH PEPTIDE PPYPAWHAPGNI
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2A6J | PDB ENTRY 2A6J |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6.5 | 0.05 M SODIUM CACODYLATE PH 6.5, 18% PEG 3000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.56 | α = 90 |
b = 76.77 | β = 102.31 |
c = 59.17 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 110 | IMAGE PLATE | MARRESEARCH | MIRRORS | 2006-05-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.89 | 57 | 97.8 | 0.12 | 9.4 | 4.7 | 10548 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.89 | 3.05 | 99.7 | 0.32 | 3.9 | 4.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 2A6J | 2.89 | 57.81 | 9490 | 1034 | 97.42 | 0.22993 | 0.22733 | 0.25419 | RANDOM | 23.643 |
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] | |
-1.04 | -1.09 | 1.4 | -0.83 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.42 |
r_dihedral_angle_4_deg | 24.759 |
r_dihedral_angle_3_deg | 18.684 |
r_dihedral_angle_1_deg | 4.382 |
r_scangle_it | 2.405 |
r_angle_refined_deg | 1.804 |
r_mcangle_it | 1.685 |
r_scbond_it | 1.473 |
r_mcbond_it | 0.916 |
r_chiral_restr | 0.136 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3381 |
Nucleic Acid Atoms | |
Solvent Atoms | 77 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |