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: 12 % / Av σ(I) over netI: 13.74 / Number: 131959 / Rmerge(I) obs: 0.183 / Χ2: 1.04 / D res high: 2.8 Å / D res low: 40 Å / Num. obs: 10977 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
6.03
40
100
1
0.182
1.457
14.5
4.79
6.03
100
1
0.129
0.995
14.9
4.18
4.79
100
1
0.13
0.985
15.2
3.8
4.18
100
1
0.162
1.041
15.2
3.53
3.8
100
1
0.216
0.99
14.5
3.32
3.53
100
1
0.275
0.99
13.2
3.15
3.32
99.9
1
0.335
0.937
11.2
3.02
3.15
98.9
1
0.38
0.903
8.8
2.9
3.02
95.5
1
0.443
0.857
6.2
2.8
2.9
85.9
1
0.455
0.917
4.6
Reflection
Resolution: 2.8→40 Å / Num. obs: 10977 / % possible obs: 98.1 % / Redundancy: 12 % / Rmerge(I) obs: 0.183 / Χ2: 1.04 / Net I/σ(I): 13.742
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
2.8-2.9
4.6
0.455
933
0.917
85.9
2.9-3.02
6.2
0.443
1061
0.857
95.5
3.02-3.15
8.8
0.38
1079
0.903
98.9
3.15-3.32
11.2
0.335
1125
0.937
99.9
3.32-3.53
13.2
0.275
1083
0.99
100
3.53-3.8
14.5
0.216
1128
0.99
100
3.8-4.18
15.2
0.162
1108
1.041
100
4.18-4.79
15.2
0.13
1133
0.985
100
4.79-6.03
14.9
0.129
1133
0.995
100
6.03-40
14.5
0.182
1194
1.457
100
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.006
dataextraction
Refinement
Resolution: 2.8→33.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.82 / SU B: 14.486 / SU ML: 0.282 / SU Rfree: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH F217 MUTATED TO A Y IN THE FIRST OF THE TWO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH F217 MUTATED TO A Y IN THE FIRST OF THE TWO HALVES. BECAUSE THE CRYSTAL IS ISOMORPHOUS WITH WTUROD IN WHICH THERE IS A MONOMER IN THE ASYMMETRIC UNIT, WE HAVE MODELED Y217 IN TWO CONFORMATIONS AT ONE-HALF OCCUPANCY EACH. THIS ACCOUNTS FOR THE STOCHASTIC ARRANGEMENT OF THE FUSION DIMER IN THE CRYSTAL SUCH THAT RESIDUE 217 IS EFFECTIVELY HALF F AND HALF Y.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.262
1067
9.7 %
RANDOM
Rwork
0.172
-
-
-
obs
0.181
10954
97.93 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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