6P6U
Crystal Structure of Monoclinic Rabbit Muscle Lactate Dehydrogenase with Four Tetramers as the Asymmetric Unit
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6LDH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | Sitting drop composed of equal amounts of 20% PEG 3350 in .10 M Tris buffer pH 7.0 and a 30 mg/ml stock protein solution containing 0.1 M Tris pH 7.0. Reservoir 20% PEG 3350 in water. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 160.572 | α = 90 |
b = 100.838 | β = 101.23 |
c = 223.102 | 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 | 298 | AREA DETECTOR | SDMS | bent crystal monochromator | 1995-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | CC (Half) | 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 | 2.4 | 60 | 88 | 0.13 | 0.12 | 0.97 | 7.4 | 6.5 | 3 | 52 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.4 | 2.45 | 22 | 0.28 | 0.28 | 0.54 | 3.3 | 3 |
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 | 6LDH | 2.42 | 60 | 123133 | 13675 | 51.51 | 0.18412 | 0.18092 | 0.21338 | RANDOM | 52.132 |
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] | |
-1.27 | 1.69 | 2.47 | -1.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.79 |
r_dihedral_angle_4_deg | 24.182 |
r_dihedral_angle_3_deg | 15.106 |
r_long_range_B_refined | 9.963 |
r_long_range_B_other | 9.963 |
r_scangle_other | 6.459 |
r_dihedral_angle_1_deg | 5.174 |
r_mcangle_it | 4.954 |
r_mcangle_other | 4.954 |
r_scbond_it | 3.908 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 40944 |
Nucleic Acid Atoms | |
Solvent Atoms | 1380 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |