2V41 | pdb_00002v41

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V2G	PDB ENTRY 2V2G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		RESERVOIR : BIS TRIS 0.1 M PH 5.5 , PEG 3350 25%(W/V). DTT 0.001 M DROP 1UL PROTEIN AND 1 UL RESERVOIR

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.11	α = 90
b = 111.156	β = 90
c = 229.8	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	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	2.4	15	99	0.06	15.2	3.7		77362

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	2.4	2.5	96.9		0.42	3.3	3.4

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	PDB ENTRY 2V2G	2.4	15	72061	3823	97.8	0.18	0.177	0.18	0.239	0.24	RANDOM	34.25

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]
-0.04			0.07		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.231
r_dihedral_angle_3_deg	17.645
r_dihedral_angle_4_deg	17.622
r_dihedral_angle_1_deg	6.791
r_scangle_it	2.607
r_scbond_it	1.863
r_angle_refined_deg	1.737
r_mcangle_it	1.051
r_angle_other_deg	1.033
r_mcbond_it	0.802
r_symmetry_vdw_refined	0.24
r_symmetry_hbond_refined	0.226
r_symmetry_vdw_other	0.21
r_nbd_refined	0.205
r_nbd_other	0.201
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.097
r_nbtor_other	0.089
r_bond_refined_d	0.02
r_gen_planes_refined	0.006
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	13593
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	72

Software

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