1ZYE

Crystal structure analysis of Bovine Mitochondrial Peroxiredoxin III

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QMV	PDB code 1qmv

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	289	ammonium sulfate, isopropanol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 300.995	α = 90
b = 80.679	β = 112.76
c = 124.295	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		2004-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9790	ESRF	BM14

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	3.3	35	100	0.122	5.1	7.5	41825	41825			80.3

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	3.3	3.5	100		0.507	1.3	7.6	6070

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code 1qmv	3.3	35	41825	39668	2109	100	0.22819	0.22819	0.22624	0.26486	RANDOM	72.896

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]
0.25		-2.14	-1.53		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.641
r_dihedral_angle_4_deg	22.797
r_dihedral_angle_3_deg	21.253
r_dihedral_angle_1_deg	6.791
r_scangle_it	2.47
r_angle_refined_deg	1.586
r_scbond_it	1.342
r_mcangle_it	1.138
r_mcbond_it	0.615
r_symmetry_vdw_refined	0.362

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.641
r_dihedral_angle_4_deg	22.797
r_dihedral_angle_3_deg	21.253
r_dihedral_angle_1_deg	6.791
r_scangle_it	2.47
r_angle_refined_deg	1.586
r_scbond_it	1.342
r_mcangle_it	1.138
r_mcbond_it	0.615
r_symmetry_vdw_refined	0.362
r_nbtor_refined	0.32
r_nbd_refined	0.235
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.12
r_chiral_restr	0.093
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15192
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.