2AV4 | pdb_00002av4

Crystal structure of Plasmodium yoelii thioredoxin-like protein 4A (DIM1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QGV	PDB ENTRY 1QGV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			295	1.4 M NaCl, pH 9.0, VAPOR DIFFUSION, temperature 295 K

Crystal Properties
Matthews coefficient	Solvent content
2.6	53.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.877	α = 90
b = 109.877	β = 90
c = 85.17	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH		2005-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM		APS	17-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.73	41.5	95.4	0.061	0.061	11.3	2.9	20820	20820

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.86	91.3		0.385	0.385	2.28	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1QGV	1.73	41.5	19950	19895	666	98.77	0.20958	0.20798	0.21	0.26115	0.21	RANDOM	20.552

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]
-0.17	-0.08		-0.17		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.611
r_dihedral_angle_4_deg	25.447
r_dihedral_angle_3_deg	13.695
r_dihedral_angle_1_deg	6.256
r_scangle_it	4.308
r_scbond_it	2.753
r_mcangle_it	1.735
r_angle_refined_deg	1.459
r_mcbond_it	1.217
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.171
r_symmetry_hbond_refined	0.168
r_chiral_restr	0.114
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1115
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
MOLREP	phasing
ARP/wARP	model building