4DSR | pdb_00004dsr

Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in reduced form

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TP9	PDB ENTRY 1TP9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	25% polyethylene glycol 3350, 0.2M ammonium sulfate, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.463	α = 90
b = 154.463	β = 90
c = 90.966	γ = 120

Symmetry
Space Group	H 3

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		2011-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9791	SSRF	BL17U

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	2.91	50	91.3	0.131	0.131	7.68	4	16465	16465		-3	70.2

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	2.91	3.01	91.5		0.369	0.369	2.991	3.4	1642

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 1TP9	2.91	44.2	15358	835	91.32	0.24051	0.23872	0.2338	0.27423	0.2671	RANDOM	62.23

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]
-1.51	-0.75		-1.51		2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.182
r_dihedral_angle_3_deg	17.59
r_dihedral_angle_4_deg	14.112
r_dihedral_angle_1_deg	7.182
r_scangle_it	1.649
r_angle_refined_deg	1.401
r_scbond_it	0.995
r_mcangle_it	0.681
r_mcbond_it	0.359
r_chiral_restr	0.098
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5328
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling