Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, GLU 58 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 59 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 58 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 59 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 278 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 289 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 280 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 58 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 59 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 278 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 279 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 280 TO ALA
Sequence details
N TERMINAL GTENLYFQSM SEQUENCE DUE TO CLONING AND UNCLEAVED TAG AND MUTATIONS E58A K59A E278A E279A K280A
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 3.15 Å3/Da / Density % sol: 60.99 % / Description: NONE
Type: MARRESEARCH / Detector: CCD / Date: Aug 11, 2010
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9795 Å / Relative weight: 1
Reflection
Resolution: 2.8→19.92 Å / Num. obs: 31699 / % possible obs: 99.7 % / Observed criterion σ(I): 1.6 / Redundancy: 5 % / Biso Wilson estimate: 94.76 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4
Reflection shell
Resolution: 2.8→2.95 Å / Redundancy: 5 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.6 / % possible all: 100
-
Processing
Software
Name
Version
Classification
BUSTER
2.8.0
refinement
XDS
datareduction
SCALA
datascaling
SHARP
phasing
Refinement
Method to determine structure: MIRAS Starting model: NONE Resolution: 2.8→29.73 Å / Cor.coef. Fo:Fc: 0.9211 / Cor.coef. Fo:Fc free: 0.8688 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=UNK. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6350. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=UNK. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6350. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2553
1607
5.07 %
RANDOM
Rwork
0.2125
-
-
-
obs
0.2146
31694
-
-
Displacement parameters
Biso mean: 73.71 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.9749 Å2
0 Å2
0 Å2
2-
-
-2.6662 Å2
0 Å2
3-
-
-
3.641 Å2
Refine analyze
Luzzati coordinate error obs: 0.453 Å
Refinement step
Cycle: LAST / Resolution: 2.8→29.73 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6249
0
6
82
6337
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
6418
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.07
8738
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2868
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
117
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
979
HARMONIC
5
X-RAY DIFFRACTION
t_it
6418
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
0
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
2.65
X-RAY DIFFRACTION
t_other_torsion
2.94
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
822
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
7133
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.8→2.89 Å / Total num. of bins used: 16
Rfactor
Num. reflection
% reflection
Rfree
0.2953
133
4.66 %
Rwork
0.2562
2724
-
all
0.2579
2857
-
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.7187
0.1387
0.2473
0.7315
-0.2203
2.5983
-0.1232
0.1451
-0.0085
-0.2194
0.1414
-0.1943
0.4789
0.0821
-0.0182
-0.063
-0.0483
0.0696
-0.3041
-0.011
-0.2141
47.3018
57.4346
63.673
2
1.2417
0.2744
0.884
1.4201
0.0532
2.1129
0.0305
-0.0671
0.0497
0.0087
-0.1083
-0.214
0.1223
0.0701
0.0779
-0.1562
0.0493
0.0124
-0.223
0.0615
-0.1764
61.0563
66.2527
98.0487
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAIN A AND (RESID -9 - 40 AND RESID 41 - 59 AND RESID 66 - 114 AND RESID 117 - 275 AND 282 - 343 AND RESID 372 - 488)
2
X-RAY DIFFRACTION
2
CHAIN B AND (RESID -2 - 40 AND RESID 41 - 274 AND RESID 282 - 343 AND RESID 373 - 487)
+
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