9G92 | pdb_00009g92

Crystal structure of thioredoxin reductase from Cryptosporidium parvum in the "in" conformation

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4J57

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	294.15	0.1 M Tris/HCl, 0.1 M KSCN, PEG 2000 MME, 5mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.866	α = 90
b = 74.323	β = 90
c = 188.748	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		2022-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	39.868	99.9	0.2	0.998	14.1	12.3		75521

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02			1.229	0.831

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	1.95	39.868	75510	3917	99.919	0.179	0.1772	0.1861	0.2123	0.219	25.013

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]
-0.769			0.061		0.708

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.454
r_dihedral_angle_4_deg	18.003
r_dihedral_angle_3_deg	12.952
r_dihedral_angle_other_3_deg	8.271
r_dihedral_angle_1_deg	7.069
r_lrange_it	5.279
r_lrange_other	5.244
r_scangle_it	4.036
r_scangle_other	4.036
r_mcangle_it	2.817
r_mcangle_other	2.816
r_scbond_it	2.665
r_scbond_other	2.664
r_mcbond_it	2.009
r_mcbond_other	2.005
r_angle_refined_deg	1.523
r_angle_other_deg	1.361
r_nbd_other	0.271
r_symmetry_nbd_refined	0.222
r_nbd_refined	0.201
r_symmetry_nbd_other	0.175
r_symmetry_xyhbond_nbd_refined	0.163
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.077
r_ncsr_local_group_1	0.073
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.009
r_bond_other_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7546
Nucleic Acid Atoms
Solvent Atoms	477
Heterogen Atoms	128

Software

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