2V2G

Crystal Structure of the C45S mutant of the Peroxiredoxin 6 of Arenicola Marina. Monoclinic form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HD2	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1NM3	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1PRX	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1QMV	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1QQ2	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1QXH	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1TP9	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1WE0	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1X0R	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1XCC	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	1ZYE	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	2CV4	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG
experimental model	PDB	2FEG	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		RESERVOIR : BIS-TRIS 0.1M PH 5.5, PEG3350 25%(W/V), DTT 0.001M, AMMONIUM SULFATE 0.1M DROP 1UL PROTEIN AND 1 UL RESERVOIR

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.246	α = 90
b = 83.226	β = 100.71
c = 98.349	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MARRESEARCH	TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING	2006-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	1.6	14	99.2	0.06	13.1	3.7		131708

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	1.6	1.7	99.2		0.62	2.2	3.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG	1.6	13.96	125024	6651	99.4	0.162	0.16	0.197	RANDOM	20.68

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.094
r_dihedral_angle_3_deg	13.508
r_dihedral_angle_4_deg	12.79
r_dihedral_angle_1_deg	6.327
r_scangle_it	3.785
r_scbond_it	2.829
r_angle_refined_deg	1.773
r_mcangle_it	1.561
r_mcbond_it	1.356
r_angle_other_deg	1.021
r_symmetry_vdw_refined	0.757
r_symmetry_vdw_other	0.237
r_nbd_refined	0.216
r_nbd_other	0.206
r_nbtor_refined	0.177
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.107
r_nbtor_other	0.088
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6791
Nucleic Acid Atoms
Solvent Atoms	1051
Heterogen Atoms	60

Software

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