#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2008 Title: Purification, crystallization and preliminary X-ray diffraction analysis of human chondroadherin. Authors: Pramhed, A. / Addis, L. / Tillgren, V. / Wenglen, C. / Heinegard, D. / Logan, D.T.
History
Deposition
Jul 3, 2016
Deposition site: PDBE / Processing site: PDBE
Revision 1.0
Dec 28, 2016
Provider: repository / Type: Initial release
Revision 1.1
Jan 11, 2017
Group: Database references
Revision 1.2
Jan 25, 2017
Group: Database references
Revision 1.3
Jan 17, 2018
Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
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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: 2.63 Å3/Da / Density % sol: 53.8 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion / pH: 9.5 Details: 21% PEG 3350, 6% xylitol, 0.1 M glycine-NaOH pH 9.5-10.5, 0.2 M ammonium sulfate. Protein at 1.2 mg/ml in 20 mM Tris pH 7.0, 200 mM NaCl. Mixed in 1:1 ratio with reservoir.
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
Detector
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2005 / Details: KB MIRRORS
Radiation
Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.1→15 Å / Num. obs: 88893 / % possible obs: 95.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 39.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.088 / Net I/σ(I): 6.7
Reflection shell
Resolution: 2.1→2.14 Å / Redundancy: 2 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.562 / % possible all: 91.1
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Processing
Software
Name
Version
Classification
PHENIX
(1.11rc2_2531: ???)
refinement
XDS
datareduction
XSCALE
datascaling
AMPLE
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: DE NOVO MODELS Resolution: 2.1→15 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2623
4467
5.04 %
Rwork
0.2449
-
-
obs
0.2457
88684
95.48 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.1→15 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
10359
0
2
120
10481
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.002
10597
X-RAY DIFFRACTION
f_angle_d
0.589
14371
X-RAY DIFFRACTION
f_dihedral_angle_d
9.765
6477
X-RAY DIFFRACTION
f_chiral_restr
0.041
1608
X-RAY DIFFRACTION
f_plane_restr
0.004
1868
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.1-2.1238
0.3831
135
0.3823
2524
X-RAY DIFFRACTION
87
2.1238-2.1488
0.418
123
0.3667
2806
X-RAY DIFFRACTION
94
2.1488-2.175
0.4
154
0.3617
2807
X-RAY DIFFRACTION
95
2.175-2.2025
0.3792
151
0.3557
2727
X-RAY DIFFRACTION
95
2.2025-2.2315
0.3509
160
0.3566
2785
X-RAY DIFFRACTION
94
2.2315-2.2621
0.3713
141
0.3498
2784
X-RAY DIFFRACTION
95
2.2621-2.2944
0.3796
162
0.3356
2706
X-RAY DIFFRACTION
94
2.2944-2.3286
0.3581
145
0.3462
2748
X-RAY DIFFRACTION
94
2.3286-2.365
0.3541
155
0.3397
2790
X-RAY DIFFRACTION
95
2.365-2.4037
0.36
130
0.3375
2763
X-RAY DIFFRACTION
94
2.4037-2.4451
0.3851
139
0.3261
2764
X-RAY DIFFRACTION
94
2.4451-2.4896
0.3574
129
0.3235
2722
X-RAY DIFFRACTION
93
2.4896-2.5374
0.3271
131
0.3139
2763
X-RAY DIFFRACTION
94
2.5374-2.5892
0.319
153
0.2992
2761
X-RAY DIFFRACTION
94
2.5892-2.6454
0.3278
140
0.2991
2728
X-RAY DIFFRACTION
93
2.6454-2.7069
0.3393
124
0.3018
2775
X-RAY DIFFRACTION
93
2.7069-2.7746
0.3128
127
0.2849
2716
X-RAY DIFFRACTION
92
2.7746-2.8495
0.263
165
0.2763
2713
X-RAY DIFFRACTION
93
2.8495-2.9333
0.3098
163
0.2803
2785
X-RAY DIFFRACTION
96
2.9333-3.0279
0.3033
157
0.2803
2902
X-RAY DIFFRACTION
100
3.0279-3.136
0.3244
167
0.264
2950
X-RAY DIFFRACTION
100
3.136-3.2613
0.2708
163
0.2588
2894
X-RAY DIFFRACTION
99
3.2613-3.4095
0.2503
155
0.237
2936
X-RAY DIFFRACTION
100
3.4095-3.5889
0.2556
166
0.2272
2927
X-RAY DIFFRACTION
100
3.5889-3.8133
0.2007
156
0.2029
2915
X-RAY DIFFRACTION
99
3.8133-4.1069
0.1843
133
0.1933
2932
X-RAY DIFFRACTION
99
4.1069-4.5187
0.2036
168
0.1869
2908
X-RAY DIFFRACTION
99
4.5187-5.1691
0.1857
165
0.1691
2936
X-RAY DIFFRACTION
99
5.1691-6.4993
0.2126
160
0.1869
2934
X-RAY DIFFRACTION
99
6.4993-15
0.2224
150
0.2083
2816
X-RAY DIFFRACTION
93
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
3.9508
0.6084
0.8605
0.9843
0.2804
1.8063
-0.0445
0.0628
0.1315
-0.0141
0.0629
0.0916
0.0398
-0.1001
0.0106
0.2067
0.0025
0.0034
0.3836
0.1088
0.2349
7.252
59.7474
95.0725
2
3.7379
-0.8147
0.9912
1.2702
-0.5223
2.0877
0.0514
-0.0332
0.2594
-0.0695
0.0018
-0.0353
0.0723
0.2368
-0.0293
0.2333
0.0222
0.0329
0.4442
-0.1778
0.3111
-6.1103
62.411
61.9234
3
1.4132
0.4756
-0.9932
1.3711
-1.3986
2.9428
-0.104
0.0518
0.0392
-0.0361
0.0956
0.0311
0.2403
0.2138
0.0254
0.2735
0.0273
-0.03
0.4247
-0.1249
0.2542
25.8348
94.499
129.9886
4
1.8538
-0.2213
-1.2169
1.2732
1.2865
3.8936
-0.1419
-0.1824
0.1081
0.0132
0.1391
0.047
0.3461
0.1033
0.0091
0.2633
0.0291
-0.059
0.2855
0.0739
0.2182
14.0653
96.5713
98.8468
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A'
2
X-RAY DIFFRACTION
2
chain 'B'
3
X-RAY DIFFRACTION
3
chain 'C'
4
X-RAY DIFFRACTION
4
chain 'D'
+
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