6RB5 | pdb_00006rb5

Trypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-6,6-dimethylbicyclo[3.1.1]heptan-2-yl)ethyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl)propyl)(methyl)amino)methyl)-4-hydroxypiperidine-1-carboximidamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WBA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	294.15	SEEDING IN 0,1 M Hepes pH 6.8; 2.1 M Ammonium Sulphate

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.073	α = 90
b = 132.622	β = 90
c = 161.052	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 PILATUS 6M		2018-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976254	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.977	102.378	99.7	0.071	0.078	0.999	13.276	5.5		94907

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.977	2.012	99.9		0.786	0.871	0.788	1.1	5.4

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	2WBA	1.977	102.378	90068	4839	99.71	0.18427	0.18309	0.19	0.20659	0.21	RANDOM	37.555

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]
0.47			-0.51		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.824
r_dihedral_angle_4_deg	12.641
r_dihedral_angle_3_deg	11.391
r_dihedral_angle_1_deg	5.772
r_long_range_B_refined	4.294
r_long_range_B_other	4.2
r_scangle_other	2.358
r_mcangle_it	1.946
r_mcangle_other	1.946
r_scbond_it	1.403
r_scbond_other	1.403
r_angle_refined_deg	1.37
r_angle_other_deg	1.285
r_mcbond_it	1.178
r_mcbond_other	1.176
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_bond_other_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	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	7440
Nucleic Acid Atoms
Solvent Atoms	487
Heterogen Atoms	368

Software

Software
Software Name	Purpose
autoPROC	data collection
XDS	data reduction
Aimless	data scaling
pointless	data scaling
STARANISO	data scaling
Coot	model building
MOLREP	phasing
REFMAC	refinement