- PDB-1zko: Crystal structure of Glycine cleavage system H protein (tm0212) f... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1zko
Title
Crystal structure of Glycine cleavage system H protein (tm0212) from Thermotoga maritima at 1.65 A resolution
Components
Glycine cleavage system H protein
Keywords
Glycine cleavage H-protein / tm0212 / Glycine cleavage system H protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information
glycine cleavage complex / glycine decarboxylation via glycine cleavage system / cytoplasm / cytosol Similarity search - Function
SEQUENCE CLONING ARTIFACT: IN THE CLONING CONSTRUCT, THE START CODON WAS CHANGED FROM ATG TO TTG. ...SEQUENCE CLONING ARTIFACT: IN THE CLONING CONSTRUCT, THE START CODON WAS CHANGED FROM ATG TO TTG. AS A RESULT, THE FIRST METHIONINE RESIDUE IS MUTATED TO LEUCINE.
Monochromator: single crystal Si(111) bent monochromator(horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.946415
1
2
0.979129
1
3
0.979494
1
Reflection
Resolution: 1.56→42.53 Å / Num. obs: 30875 / % possible obs: 87.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 6.4
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Rsym value
% possible all
1.56-1.64
1.7
0.367
2
2019
0.367
40
1.64-1.74
3.5
0.321
2.3
4751
0.321
98.4
1.74-1.86
3.9
0.226
3.3
4547
0.226
99.5
1.86-2.01
3.9
0.149
4.9
4169
0.149
98.7
2.01-2.21
3.8
0.098
6.8
3770
0.098
96.6
2.21-2.47
3.8
0.074
8.6
3327
0.074
93.6
2.47-2.85
3.7
0.065
8.9
2892
0.065
91.7
2.85-3.49
3.6
0.051
10.9
2396
0.051
89.6
3.49-4.93
3.6
0.043
11.1
1889
0.043
89.8
4.93-42.53
3.5
0.036
11.7
1115
0.036
93
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
1.601
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
autoSHARP
phasing
SHELXL
refinement
Refinement
Method to determine structure: MAD / Resolution: 1.65→42.53 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.538 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.135 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. THE R AND R-FREE FACTORS ARE HIGH DESPITE THE RESOLUTION. ONE REASON MAY BE THAT THE DIFFRACTION IMAGES SHOW DIFFRACTION FROM MORE THAN ONE CRYSTAL. THE ELECTRON DENSITY MAPS ARE VERY ...Details: 1. THE R AND R-FREE FACTORS ARE HIGH DESPITE THE RESOLUTION. ONE REASON MAY BE THAT THE DIFFRACTION IMAGES SHOW DIFFRACTION FROM MORE THAN ONE CRYSTAL. THE ELECTRON DENSITY MAPS ARE VERY CLEAR FOR THE TWO MONOMERS IN THE ASYMMETRIC UNIT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27
1433
5 %
RANDOM
Rwork
0.225
-
-
-
all
0.227
-
-
-
obs
0.22724
26956
94.6 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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