6THL | pdb_00006thl

Crystal structure of the complex between RTT106 and BCD1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TW1	3TW1, 6NZ2
experimental model	PDB	6NZ2	3TW1, 6NZ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Drops were made at 293 K by mixing the protein solution at 10 mg/mL and the reservoir solution containing 10 % (w/v) PEG 8K, 20 % (v/v) ethylene glycol, 10 mM 1,6-hexanediol, 10 mM 2-propanol and 100 mM sodium HEPES at pH 7.5.

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.712	α = 90
b = 66.684	β = 104.72
c = 65.122	γ = 90

Symmetry
Space Group	P 1 21 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 S 6M		2017-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.033	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.79	50	99.1	0.047	27.4	6.7		11730

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.95			0.201

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	3TW1, 6NZ2	2.8	19.86	10224	1135	96.94	0.2191	0.21	0.2178	0.2997	0.298	RANDOM	58.036

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]
0.09		0.07	-0.05		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.282
r_dihedral_angle_4_deg	22.067
r_dihedral_angle_3_deg	18.446
r_dihedral_angle_1_deg	8.126
r_angle_refined_deg	1.74
r_angle_other_deg	0.82
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3007
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XPREP	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction