5OJM | pdb_00005ojm

Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4COF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	277.15	14% poly-ethylene glycol (PEG) 5000, 0.08M magnesium acetate, 0.1M sodium citrate, 1mM ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA)

Crystal Properties
Matthews coefficient	Solvent content
3.93	68.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.35	α = 90
b = 139.94	β = 102.25
c = 191.5	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2015-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.3	48.88	99.78	0.352	0.116	0.998	7.85	10		68852			87.76

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.418	99.71		2.807	0.935	0.395	1.08	9.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4COF	3.3	48.88	48360	2506	73.58	0.23449	0.2337	0.25	0.2496	0.27	RANDOM	70.037

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-2.2		1.92	-1.67		2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.368
r_dihedral_angle_3_deg	14.586
r_dihedral_angle_4_deg	13.697
r_long_range_B_refined	8.763
r_long_range_B_other	8.763
r_dihedral_angle_1_deg	7.236
r_scangle_other	4.37
r_mcangle_it	3.682
r_mcangle_other	3.682
r_scbond_it	2.677
r_scbond_other	2.677
r_mcbond_it	2.235
r_mcbond_other	2.235
r_angle_refined_deg	0.71
r_angle_other_deg	0.501
r_chiral_restr	0.054
r_gen_planes_refined	0.012
r_bond_refined_d	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18141
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	397

Software

Software
Software Name	Purpose
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PHENIX	refinement
Coot	model building