RhoGTPase-activatingprotein7 / Rho-type GTPase-activating protein 7 / Deleted in liver cancer 1 protein / Dlc-1 / StAR-related ...Rho-type GTPase-activating protein 7 / Deleted in liver cancer 1 protein / Dlc-1 / StAR-related lipid transfer protein 12 / START domain-containing protein 12 / StARD12 / HP protein
Mass: 26038.930 Da / Num. of mol.: 1 / Fragment: Rho-GAP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLC1, ARHGAP7, KIAA1723, STARD12 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q96QB1
Resolution: 2.3→48.75 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.188 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The programs CHAINSAW, PHENIX, ARP/WARP, COOT and MOLPROBITY were also used during refinement.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26028
584
4.8 %
RANDOM
Rwork
0.21615
-
-
-
obs
0.21821
11699
98.14 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 20.67 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.19 Å2
0 Å2
0 Å2
2-
-
1.96 Å2
0 Å2
3-
-
-
-0.77 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→48.75 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1508
0
4
30
1542
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
1534
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1011
X-RAY DIFFRACTION
r_angle_refined_deg
1.437
1.974
2083
X-RAY DIFFRACTION
r_angle_other_deg
0.916
3
2480
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.627
5
192
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.27
25.135
74
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.144
15
264
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.561
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
241
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
1710
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
291
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.721
1.5
962
X-RAY DIFFRACTION
r_mcbond_other
0.151
1.5
383
X-RAY DIFFRACTION
r_mcangle_it
1.421
2
1546
X-RAY DIFFRACTION
r_scbond_it
2.418
3
572
X-RAY DIFFRACTION
r_scangle_it
4.101
4.5
536
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.366
36
-
Rwork
0.259
765
-
obs
-
-
89.2 %
+
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