Mass: 9699.214 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K561 / Gene: GEN V IN BACTERIOPHAGE F1 / Plasmid: PTT2 / Gene (production host): GEN V / Production host: Escherichia coli (E. coli) / Strain (production host): K561 / References: UniProt: P69543
Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal grow
Method: vapor diffusion / pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM SOLUTIONS CONTAINING 10 MG/ML PROTEIN, 4 MM TRIS BUFFER (PH7.5), AND 16% PEG 4000 (W/V), EQUILIBRATED AGAINST 12% PEG 4000 BY VAPOR DIFFUSION AT ROOM TEMPERATURE., vapor diffusion
Resolution: 1.6→8 Å / Num. obs: 9073 / % possible obs: 77.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.043
Reflection shell
Resolution: 1.6→2 Å / % possible all: 60.8
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Processing
Software
Name
Version
Classification
X-PLOR
3.1
modelbuilding
X-PLOR
3.1
refinement
R-AXIS
IIC
datareduction
R-AXIS
II
datascaling
X-PLOR
3.1
phasing
Refinement
Method to determine structure: DIFFERENCE FOURIERS / Resolution: 1.6→8 Å / Rfactor Rfree error: 0.0094 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: MEAN B FACTOR INCLUDES THE CONTRIBUTION FROM ALL HYDROGEN ATOMS. THE B-FACTORS OF ALL HYDROGEN ATOMS IN WATER ARE SET TO 35.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.288
941
10.4 %
RANDOM
Rwork
0.209
-
-
-
obs
0.209
9016
77.9 %
-
Displacement parameters
Biso mean: 29.6 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.4616 Å2
0 Å2
2.8596 Å2
2-
-
-0.996 Å2
0 Å2
3-
-
-
1.4576 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.3 Å
0.23 Å
Luzzati d res low
-
6 Å
Refinement step
Cycle: LAST / Resolution: 1.6→8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
682
0
0
53
735
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
x_bond_d
0.017
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
3.4
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
27.63
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
1.39
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
2.5
1.5
X-RAY DIFFRACTION
x_mcangle_it
4.15
2
X-RAY DIFFRACTION
x_scbond_it
4.21
2
X-RAY DIFFRACTION
x_scangle_it
6.76
2.5
LS refinement shell
Resolution: 1.6→1.67 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 8
Rfactor
Num. reflection
% reflection
Rfree
0.4057
49
9.5 %
Rwork
0.3812
468
-
obs
-
-
35.4 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
PARAM19XM.PRO
TOPH19X.PRO
X-RAY DIFFRACTION
2
+
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