AUTHORS STATE THAT THE SEQUENCE REGISTRY OF LD2 PEPTIDE CHAIN B WAS BASED ON HOMOLOGY WITH PREVIOUS ...AUTHORS STATE THAT THE SEQUENCE REGISTRY OF LD2 PEPTIDE CHAIN B WAS BASED ON HOMOLOGY WITH PREVIOUS CRYSTAL STRUCTURES OF FAK FOCAL ADHESION TARGETING (FAT) DOMAIN IN COMPLEX WITH PAXILLIN LD2 PEPTIDE (1OW8; COMPLEX A/D) AND PYK2 FOCAL ADHESION TARGETING (FAT) DOMAIN IN COMPLEX WITH PAXILLIN LD4 PEPTIDE (3GM1; COMPLEXS A/E AND B/C).
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 6.26 Å3/Da / Density % sol: 80.37 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: THE WELL SOLUTION CONTAINED 100 mM TRIS, 2.0 M AMMONIUM PHOSPHATE MONOBASIC. THE 4 UL DROP CONTAINED 2 uL OF WELL SOLUTION PLUS 2 uL MIXTURE OF PYK2 AND LD2 IN 20 MM MES, PH 6.0, AT 1 mM ...Details: THE WELL SOLUTION CONTAINED 100 mM TRIS, 2.0 M AMMONIUM PHOSPHATE MONOBASIC. THE 4 UL DROP CONTAINED 2 uL OF WELL SOLUTION PLUS 2 uL MIXTURE OF PYK2 AND LD2 IN 20 MM MES, PH 6.0, AT 1 mM PROTEIN TO 2 mM PEPTIDE RATIO , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution: 3.5→3.62 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.272 / % possible all: 5.4
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Processing
Software
Name
Version
Classification
MAR345dtb
datacollection
PHASER
phasing
PHENIX
(phenix.refine: dev_1730)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.505→28.934 Å / SU ML: 0.35 / σ(F): 1.38 / Phase error: 24.86 / Stereochemistry target values: ML Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY. REFINEMENT WAS PERFORMED AGAINST ELLIPTICALLY TRUNCATED DATA (RESOLUTION LIMITS OF 1/3.8, 1/3.8, AND 1/3.5 A2 IN A*, B*, C*, ...Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY. REFINEMENT WAS PERFORMED AGAINST ELLIPTICALLY TRUNCATED DATA (RESOLUTION LIMITS OF 1/3.8, 1/3.8, AND 1/3.5 A2 IN A*, B*, C*, RESPECTIVELY) CORRECTED BY ANISOTROPIC SCALE FACTORS AND AN ISOTROPIC B OF -33.95 A2 USING THE UCLA DIFFRACTION ANISOTROPY SERVER (STRONG ET AL., 2006).
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2398
264
4.61 %
Random
Rwork
0.2208
-
-
-
obs
0.2217
5731
82.7 %
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all
-
5731
-
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 3.505→28.934 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1104
0
0
0
1104
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
1108
X-RAY DIFFRACTION
f_angle_d
0.971
1515
X-RAY DIFFRACTION
f_dihedral_angle_d
17.911
691
X-RAY DIFFRACTION
f_chiral_restr
0.033
206
X-RAY DIFFRACTION
f_plane_restr
0.003
195
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.505-4.4136
0.2984
108
0.243
2078
X-RAY DIFFRACTION
65
4.4136-28.9351
0.2182
156
0.2129
3389
X-RAY DIFFRACTION
100
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
2.9879
1.2846
5.2712
0.5482
2.2543
9.3057
-0.407
2.1509
-0.5331
-2.2679
0.29
0.6589
0.6536
-2.2693
-0.0427
1.2799
-1.6262
0.0839
2.0501
-0.1407
1.1688
50.4503
-71.6648
-11.4924
2
5.8459
1.036
-2.0492
1.6507
-0.1731
3.3905
0.0923
0.1461
0.406
0.2039
-0.0121
0.103
0.5754
-0.0828
-0.0639
0.5543
-0.2883
-0.061
0.9815
0.0356
0.5087
68.2349
-65.5632
-3.075
3
-0.0077
0.0167
0.0075
-0.0021
-0.0092
-0.0135
-0.0421
-0.0226
-1.3026
0.2194
0.1816
0.127
2.0642
-0.4636
-0.0365
2.322
-1.2791
0.835
-0.3194
0.2355
1.3471
66.6413
-77.7475
-10.8782
4
0.0568
-0.2831
-0.0865
1.8955
0.6071
0.1817
0.6402
-0.6714
2.3003
0.2167
0.7444
0.2197
-0.1387
0.0775
-1.1653
0.7146
0.0414
-0.0073
1.1613
0.0147
1.6317
68.8658
-52.9595
-0.2798
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid873through878 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid879through1004 )
3
X-RAY DIFFRACTION
3
chain 'B' and (resid143through153 )
4
X-RAY DIFFRACTION
4
chain 'C' and (resid140through154 )
+
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