1KHP
Monoclinic form of papain/ZLFG-DAM covalent complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PPN | PDB ENTRY 1PPN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9.2 | 292 | 68% methanol/ethanol (2:1), 34 mM NaCl, 50 mM 2-aminoethanol/HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.44 | α = 90 |
b = 48.93 | β = 112.42 |
c = 52.69 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 293 | IMAGE PLATE | MARRESEARCH | 1998-03-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | MACSCIENCE | 1.5418 |
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 | 2 | 20 | 88.9 | 0.123 | 6.6 | 4.8 | 12041 | 12041 | -3 | -3 | 26.2 |
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 | 2 | 2.07 | 75.1 | 0.328 | 2 | 1.74 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1PPN | 2 | 10 | 10783 | 10783 | 1165 | 88.8 | 0.185 | 0.185 | 0.18 | 0.229 | RANDOM | 22.1 |
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] | |
-1.22 | 0.12 | 0.57 | 0.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_scangle_it | 3.784 |
p_scbond_it | 2.451 |
p_angle_deg | 1.663 |
p_mcangle_it | 1.3 |
p_mcbond_it | 0.793 |
p_chiral_restr | 0.108 |
p_angle_d | 0.025 |
p_bond_d | 0.016 |
p_plane_restr | 0.007 |
p_planar_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1679 |
Nucleic Acid Atoms | |
Solvent Atoms | 53 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |