4KIA
Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FEZ | PDB ENTRY 3FEZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.6 | 287 | 25% PEG 3350, 0.1M sodium citrate, 0.2M ammonium sulfate, pH 5.6, MICROBATCH, temperature 287K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.81 | 32.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 26.61 | α = 90 |
b = 59.474 | β = 94.57 |
c = 45.434 | 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 | CCD | ADSC QUANTUM 315r | 2009-02-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.0 | SPring-8 | BL38B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.75 | 50 | 99 | 0.064 | 30.41 | 3.6 | 14344 | 14209 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.75 | 1.81 | 94 | 0.165 | 0.166 | 5.78 | 3 |
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 | COOT and PROCHECK | PDB ENTRY 3FEZ | 1.75 | 45.29 | 14209 | 13479 | 713 | 99.06 | 0.19101 | 0.18828 | 0.24432 | RANDOM | 16.237 |
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] | |
-0.01 | 0.04 | -0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.055 |
r_dihedral_angle_3_deg | 12.699 |
r_dihedral_angle_4_deg | 7.734 |
r_sphericity_free | 5.835 |
r_dihedral_angle_1_deg | 5.761 |
r_scangle_it | 4.733 |
r_scbond_it | 3.213 |
r_sphericity_bonded | 3.146 |
r_mcangle_it | 2.023 |
r_rigid_bond_restr | 1.98 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1253 |
Nucleic Acid Atoms | |
Solvent Atoms | 96 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
DM | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
DM | phasing |