9GKG | pdb_00009gkg

Crystal structure of UNC119 in complex with Squarunkin A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6H6A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	30% w/v PEG3350 100 mM Sodium acetate pH 4.6 200-mM ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.73	α = 90
b = 80.63	β = 90
c = 191.03	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2019-09-22	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)	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	2.21	74.395	100	0.998	10.6	6.7		61768

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.27			0.626

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.21	74.395	61692	3200	99.947	0.224	0.2223	0.2273	0.2574	0.2623	44.522

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]
1.396			1.474		-2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.811
r_dihedral_angle_3_deg	15.297
r_lrange_it	8.651
r_lrange_other	8.648
r_dihedral_angle_1_deg	7.532
r_scangle_it	6.388
r_scangle_other	6.387
r_mcangle_it	5.258
r_mcangle_other	5.257
r_dihedral_angle_2_deg	4.977
r_scbond_it	4.036
r_scbond_other	4.035
r_mcbond_it	3.537
r_mcbond_other	3.533
r_angle_refined_deg	0.727
r_angle_other_deg	0.289
r_symmetry_nbd_other	0.222
r_nbd_other	0.217
r_nbd_refined	0.199
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.151
r_ncsr_local_group_5	0.126
r_ncsr_local_group_15	0.121
r_ncsr_local_group_14	0.113
r_ncsr_local_group_12	0.112
r_ncsr_local_group_9	0.11
r_ncsr_local_group_2	0.109
r_ncsr_local_group_3	0.106
r_ncsr_local_group_1	0.104
r_ncsr_local_group_8	0.104
r_ncsr_local_group_6	0.103
r_ncsr_local_group_11	0.103
r_ncsr_local_group_13	0.103
r_symmetry_nbd_refined	0.096
r_ncsr_local_group_10	0.093
r_ncsr_local_group_4	0.089
r_ncsr_local_group_7	0.088
r_symmetry_xyhbond_nbd_refined	0.085
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.045
r_symmetry_xyhbond_nbd_other	0.044
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8162
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing