4UP3 | pdb_00004up3

Crystal structure of the mutant C140S,C286Q thioredoxin reductase from Entamoeba histolytica

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A65	PDB ENTRY 4A65

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.9		0.2M LITHIUM ACETATE DIHYDRATE, 20% PEG 3350, PH 7.9

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.775	α = 90
b = 92.048	β = 90
c = 102.945	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	110	CCD	MARRESERCH	MIRRORS	2014-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.44	102.94	81.2	0.04	15	3.7		91837		0.5	23

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.44	1.52	36.4		0.54	1.3	2.2

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4A65	1.44	68.62	87129	4584	80.81	0.12866	0.12596	0.14	0.18073	RANDOM	24.825

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]
-0.11			-0.02		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.96
r_sphericity_free	22.644
r_dihedral_angle_4_deg	17.152
r_dihedral_angle_3_deg	12.511
r_sphericity_bonded	9.996
r_dihedral_angle_1_deg	6.019
r_rigid_bond_restr	5.978
r_scbond_it	4.155
r_mcangle_it	2.8
r_mcbond_it	2.533
r_mcbond_other	2.519
r_angle_refined_deg	2.032
r_angle_other_deg	0.946
r_chiral_restr	0.123
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4702
Nucleic Acid Atoms
Solvent Atoms	767
Heterogen Atoms	206

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing