porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process ...porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / nucleoplasm / cytosol Similarity search - Function
Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 18, 2008 / Details: yale mirrors
Radiation
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Redundancy: 5.3 % / Av σ(I) over netI: 17.19 / Number: 258037 / Rmerge(I) obs: 0.076 / Χ2: 1 / D res high: 1.7 Å / D res low: 40 Å / Num. obs: 48712 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
3.66
40
99.4
1
0.059
1.041
5.7
2.91
3.66
99.9
1
0.064
1.019
5.8
2.54
2.91
100
1
0.086
1.005
5.8
2.31
2.54
100
1
0.109
1.029
5.8
2.14
2.31
100
1
0.134
1.025
5.6
2.02
2.14
99.9
1
0.165
1.027
5.4
1.91
2.02
99.3
1
0.218
1.011
5.3
1.83
1.91
99
1
0.336
1.108
5.1
1.76
1.83
98.7
1
0.431
0.831
5
1.7
1.76
96.9
1
0.476
0.702
3.3
Reflection
Resolution: 1.7→40 Å / Num. obs: 48712 / % possible obs: 99.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.076 / Χ2: 0.996 / Net I/σ(I): 17.191
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.7-1.76
3.3
0.476
4670
0.702
1
96.9
1.76-1.83
5
0.431
4802
0.831
1
98.7
1.83-1.91
5.1
0.336
4809
1.108
1
99
1.91-2.02
5.3
0.218
4845
1.011
1
99.3
2.02-2.14
5.4
0.165
4873
1.027
1
99.9
2.14-2.31
5.6
0.134
4868
1.025
1
100
2.31-2.54
5.8
0.109
4886
1.029
1
100
2.54-2.91
5.8
0.086
4926
1.005
1
100
2.91-3.66
5.8
0.064
4939
1.019
1
99.9
3.66-40
5.7
0.059
5094
1.041
1
99.4
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.006
dataextraction
Refinement
Resolution: 1.7→33.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.822 / SU B: 2.22 / SU ML: 0.073 / SU R Cruickshank DPI: 0.096 / SU Rfree: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.238
1507
3.1 %
RANDOM
Rwork
0.184
-
-
-
obs
0.185
48389
99.05 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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