Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
-
Sample preparation
Crystal
Density Matthews: 2.42 Å3/Da / Density % sol: 49.26 % Description: TWO DATA SETS WERE COMBINED TO OBTAIN FINAL SET. TWO CRYSTALS WERE USED FOR DATA COLLECTION. DATA FROM 15.0 -2.24A WAS COLLECTED AT CHESS A1.(CRYSTAL DIFFRACTED TO 1.7A). DATA FROM 2.24- ...Description: TWO DATA SETS WERE COMBINED TO OBTAIN FINAL SET. TWO CRYSTALS WERE USED FOR DATA COLLECTION. DATA FROM 15.0 -2.24A WAS COLLECTED AT CHESS A1.(CRYSTAL DIFFRACTED TO 1.7A). DATA FROM 2.24-1.50A WAS COLLECTED AT CHESS F1. SEE JBC (99) ARTICLE FOR DETAILS.
Crystal grow
pH: 7 Details: PROTEIN BOUND TO GPPNHP WAS CRYSTALLIZED IN 1.8-2.0M (NH4)2SO3, 100MM SODIUM ACETATE, H 6.0, 1MM MGSO4, 1MM GPPNHP, AND 5MM DTT. PRIOR TO DATA COLLECTION CRYSTALS WERE TRANSFERED TO 2.0M ...Details: PROTEIN BOUND TO GPPNHP WAS CRYSTALLIZED IN 1.8-2.0M (NH4)2SO3, 100MM SODIUM ACETATE, H 6.0, 1MM MGSO4, 1MM GPPNHP, AND 5MM DTT. PRIOR TO DATA COLLECTION CRYSTALS WERE TRANSFERED TO 2.0M LI2SO4, 1MM GPPNHP, 3MM DTT, 1MM MGSO4, 100MM BES, PH 7.0, AND 15% GLYCEROL. CRYSTALS WERE FLASH FROZEN IN LIQUID PROPANE.
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
ID
Conc.
Common name
Crystal-ID
Sol-ID
Chemical formula
1
10mg/ml
protein
1
drop
2
1.4M
potassiumphosphate
1
drop
3
25mM
EPPS
1
drop
4
1mM
1
drop
MgSO4
6
2.5mM
dithiothreitol
1
drop
7
10mM
EDTA
1
drop
8
100mM
1
reservoir
NaCl
9
1.45-1.65 M
potassiumphosphate
1
reservoir
5
GppNHp
1
drop
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
1
Diffraction source
Source
Site
Beamline
ID
Wavelength
SYNCHROTRON
CHESS
A1
1
0.91
SYNCHROTRON
CHESS
F1
2
0.918
Detector
Type
ID
Detector
Date
ADSC QUANTUM 4
1
CCD
Jun 1, 1998
ADSC QUANTUM 4
2
CCD
Jun 1, 1998
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91
1
2
0.918
1
Reflection
Resolution: 1.5→15 Å / Num. all: 57771 / Num. obs: 57771 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 3.92 % / Biso Wilson estimate: 15.94 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.6
Reflection shell
Resolution: 1.5→1.55 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 7.5 / % possible all: 77.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 77.4 %
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Processing
Software
Name
Version
Classification
X-PLOR
modelbuilding
X-PLOR
3.851
refinement
DENZO
datareduction
SCALEPACK
datascaling
X-PLOR
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GIA
Resolution: 1.5→15 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 Details: RESIDUES 2 - 31, AND 348 - 354 ARE DISORDERED AND DID NOT APPEAR IN THE DENSITY. SIDE- CHAINS THAT ARE PARTIALLY DISORDERED HAVE THE OCCUPANCYS OF RELEVANT ATOMS SET TO 0.00.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.235
2895
4.6 %
RANDOM
Rwork
0.213
-
-
-
obs
-
57291
90.84 %
-
Displacement parameters
Biso mean: 18.02 Å2
Refinement step
Cycle: LAST / Resolution: 1.5→15 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2543
0
33
157
2733
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
x_bond_d
0.011
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
1.37
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
22.83
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
1.36
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
1.368
1.5
X-RAY DIFFRACTION
x_mcangle_it
2.166
2
X-RAY DIFFRACTION
x_scbond_it
2.619
2
X-RAY DIFFRACTION
x_scangle_it
4.17
2.5
LS refinement shell
Resolution: 1.5→1.57 Å / Total num. of bins used: 8
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