Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Sequence details
A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. In THE ENTITY 2, GPHM ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. In THE ENTITY 2, GPHM AMINO ACIDS HAVE BEEN ADDED AT THE N TERMINAL.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 4.27 Å3/Da / Density % sol: 71.22 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.49M NaH2PO4, 0.91M K2HPO4, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.625 / Num. unique all: 5598 / Rsym value: 0.669 / % possible all: 89.5
-
Processing
Software
Name
Classification
HKL-2000
datacollection
PHENIX
modelbuilding
PHENIX
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.6→30.7 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.77 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2641
3144
5.07 %
RANDOM
Rwork
0.2247
-
-
-
obs
0.2267
61951
98.69 %
-
all
-
61972
-
-
Solvent computation
Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.228 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
14.6874 Å2
-0 Å2
9.8465 Å2
2-
-
-16.2021 Å2
-0 Å2
3-
-
-
1.5148 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→30.7 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7499
0
0
43
7542
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
7623
X-RAY DIFFRACTION
f_angle_d
1.181
10305
X-RAY DIFFRACTION
f_dihedral_angle_d
15.47
2972
X-RAY DIFFRACTION
f_chiral_restr
0.072
1203
X-RAY DIFFRACTION
f_plane_restr
0.005
1322
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection obs
% reflection obs (%)
2.6-2.633
0.4382
119
0.3643
2204
2323
81
2.633-2.6761
0.3459
143
0.3358
2632
2775
98
2.6761-2.7222
0.4065
131
0.3276
2676
2807
99
2.7222-2.7717
0.3714
166
0.3132
2681
2847
99
2.7717-2.825
0.337
132
0.3004
2676
2808
99
2.825-2.8826
0.3159
139
0.2778
2668
2807
100
2.8826-2.9452
0.3546
147
0.2866
2693
2840
99
2.9452-3.0137
0.2965
127
0.2773
2706
2833
99
3.0137-3.089
0.2871
152
0.2707
2654
2806
99
3.089-3.1724
0.3175
144
0.2645
2698
2842
99
3.1724-3.2657
0.3433
153
0.2654
2696
2849
99
3.2657-3.3709
0.2789
140
0.2377
2684
2824
100
3.3709-3.4913
0.2816
151
0.2322
2694
2845
100
3.4913-3.6308
0.2408
135
0.2178
2724
2859
100
3.6308-3.7958
0.242
141
0.216
2673
2814
100
3.7958-3.9955
0.2277
141
0.1977
2706
2847
100
3.9955-4.2453
0.2339
131
0.1831
2731
2862
100
4.2453-4.5721
0.2297
161
0.1772
2700
2861
100
4.5721-5.0304
0.2166
131
0.1914
2715
2846
100
5.0304-5.7541
0.298
159
0.2311
2724
2873
100
5.7541-7.2339
0.281
142
0.2459
2723
2865
100
7.2339-30.7026
0.1939
159
0.1768
2749
2908
99
+
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