small GTPase binding => GO:0031267 / activation of GTPase activity / GTPase activator activity / intracellular protein transport / endocytosis / regulation of protein localization / early endosome / Golgi apparatus / nucleus Similarity search - Function
Rab GTPase-activating protein 1-like / Ypt/Rab-GAP domain of gyp1p, domain 1 / putative rabgap domain of human tbc1 domain family member 14 like domains / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Kinesin-like ...Rab GTPase-activating protein 1-like / Ypt/Rab-GAP domain of gyp1p, domain 1 / putative rabgap domain of human tbc1 domain family member 14 like domains / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Kinesin-like / Kinesin protein / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Cyclin A; domain 1 / Helicase, Ruva Protein; domain 3 / PH-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Redundancy: 6.5 % / Av σ(I) over netI: 31.89 / Number: 164733 / Rmerge(I) obs: 0.079 / Χ2: 3.52 / D res high: 2.7 Å / D res low: 30 Å / Num. obs: 25196 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
5.8
30
99.6
1
0.064
9.235
6.7
4.61
5.8
100
1
0.074
5.347
7
4.03
4.61
100
1
0.068
3.625
7.2
3.66
4.03
100
1
0.087
3.597
6.9
3.4
3.66
99.9
1
0.111
2.983
7.1
3.2
3.4
100
1
0.135
2.209
7.2
3.04
3.2
100
1
0.176
1.61
7
2.91
3.04
98.1
1
0.216
1.373
6.2
2.8
2.91
93.2
1
0.27
1.382
5.2
2.7
2.8
83.8
1
0.295
1.46
4.4
Reflection
Resolution: 2.3→30 Å / Num. obs: 38070 / % possible obs: 88.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 31.893
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
% possible all
2.3-2.38
2
0.233
49.8
2.38-2.48
2.4
0.206
65.5
2.48-2.59
2.8
0.181
80.6
2.59-2.73
3.2
0.152
91.9
2.73-2.9
3.5
0.116
97.8
2.9-3.12
3.6
0.092
99.3
3.12-3.43
3.8
0.072
99.6
3.43-3.93
3.9
0.058
99.7
3.93-4.95
4.1
0.05
99.9
4.95-30
4.1
0.035
99.3
-
Phasing
Phasing
Method: sad
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHELX
phasing
RESOLVE
phasing
REFMAC
5.5.0072
refinement
PDB_EXTRACT
3.006
dataextraction
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 17.965 / SU ML: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED. DM, RESOLVE, CHAINSAW, RESOLVE, PHENIX, TLSMD, COOT, MOLPROBITY WERE ALSO USED FOR PHASE IMPROVEMENT AND/OR MODEL REFINEMENT.
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