3TJF | pdb_00003tjf

Crystal Structure of human peroxiredoxin IV C51A mutant in reduced form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PN8	PDB ENTRY 2PN8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	1.55 M ammonium sulfate, 12% glycerol, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.348	α = 90
b = 138.849	β = 103.97
c = 96.236	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	ADSC QUANTUM 315r	MIRRORS	2010-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97	Diamond	I03

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	2.04	28.97	99.4	0.051	16.3	4.3	87136	87136			33.8

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	2.04	2.09	96.4		0.708	2.2	4	6233

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 (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 2PN8	2.04	28.77	87117	82773	4344	99.33	0.16152	0.16152	0.15965	0.1611	0.19711	0.2001	RANDOM	41.144

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]
1.9		-0.85	-0.17		-2.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.853
r_dihedral_angle_4_deg	15.421
r_dihedral_angle_3_deg	15.202
r_dihedral_angle_1_deg	6.089
r_scangle_it	3.546
r_scbond_it	2.249
r_angle_refined_deg	1.458
r_mcangle_it	1.393
r_mcbond_it	0.769
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7819
Nucleic Acid Atoms
Solvent Atoms	794
Heterogen Atoms	75

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement