1ZLX
The apo structure of human glycinamide ribonucleotide transformylase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GAR | Truncated (70% remaining) E. coli Glycinamide ribonucleotide transformylase 1GAR |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 300 | 5 mg/ml protein in 10 mM Hepes pH 7.5, 1 mM DTE 1:1 with well solution (100 mM Na citrate pH 6.0, 20% 2-propanol (v/v), 20% PEG-4000 (w/v)), VAPOR DIFFUSION, HANGING DROP, temperature 300K |
2 | VAPOR DIFFUSION, SITTING DROP | 6.3 | 300 | 5 mg/ml protein in 10 mM Hepes pH 7.5, 1 mM DTE 1:1 with well solution (100 mM Na citrate pH 6.0, 10% 2-propanol (v/v), 18% PEG-4000 (w/v)), pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.66 | α = 90 |
b = 75.66 | β = 90 |
c = 101.69 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | 300 | IMAGE PLATE | RIGAKU RAXIS IIC | 1996-08-16 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 110 | CCD | ADSC QUANTUM 4 | 1997-08-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
2 | SYNCHROTRON | CHESS BEAMLINE F2 | 0.68 | CHESS | F2 |
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 | ||||||||
1,2 | 2.05 | 40.2 | 75.8 | 0.089 | 8.3 | 6.9 | 20705 | 16557 | 2 | 1 | 56.2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1,2 | 2.05 | 2.15 | 3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | Truncated (70% remaining) E. coli Glycinamide ribonucleotide transformylase 1GAR | 2.2 | 40.2 | 2 | 2 | 16557 | 15686 | 871 | 80 | 0.224 | 0.267 | Selected | 56.2 |
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] | |
-7.51 | -3.13 | -7.51 | 15.03 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_mcbond_it | 4.47 |
c_angle_deg | 1.34 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1507 |
Nucleic Acid Atoms | |
Solvent Atoms | 213 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
X-PLOR | refinement |