7K35
EQADH-NADH-4-METHYLBENZYL ALCOHOL, p21
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5VL0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICRODIALYSIS | 7 | 278 | 10 MG/ML ENZYME DIALYZED AGAINST 50 MM AMMONIUM N-[TRIS(HYDROXYLMETHYL)METHYL]2-AMINOETHANE SULFONATE (PH 6.7 AT 25 DEG C) WITH 1 MM NAD+ AND 10 MM 4-METHY-BENZYL ALCOHOL AS THE CONCENTRATION OF 2-METHYL-2,4-PENTANEDIOL WAS RAISED TO 25 %. CRYSTAL WAS MOUNTED ON A FIBER LOOP AND FLASH VITRIFIED BY PLUNGING IT INTO LIQUID N2. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.22 | α = 90 |
b = 180.22 | β = 106.12 |
c = 86.86 | 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 | 100 | CCD | MARMOSAIC 300 mm CCD | 2006-07-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.9537 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.2 | 19.96 | 99.2 | 0.114 | 0.12 | 7.1 | 9.53 | 456390 | 15.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.2 | 1.24 | 98.2 | 0.596 | 0.643 | 7.2 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5vl0 | 1.2 | 19.96 | 456320 | 2399 | 99.197 | 0.177 | 0.1764 | 0.2102 | 23.888 |
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] | |
3.305 | 1.473 | -3.051 | -0.947 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.358 |
r_dihedral_angle_4_deg | 13.115 |
r_dihedral_angle_3_deg | 11.728 |
r_dihedral_angle_1_deg | 6.7 |
r_rigid_bond_restr | 4.132 |
r_scangle_it | 2.809 |
r_scangle_other | 2.809 |
r_scbond_it | 2.644 |
r_scbond_other | 2.644 |
r_lrange_it | 2.503 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11140 |
Nucleic Acid Atoms | |
Solvent Atoms | 1248 |
Heterogen Atoms | 236 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
REFMAC | phasing |