1XW3 | pdb_00001xw3

Crystal Structure of Human Sulfiredoxin (Srx)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SEMET MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	293	MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.9	56.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.057	α = 90
b = 68.057	β = 90
c = 51.302	γ = 120

Symmetry
Space Group	P 32 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	RIGAKU SATURN 92	CONFOCAL BLUE MAX-FLUX	2004-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	1.65	38.7	98.9	0.039	27.1	7.22		16690

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)
	1.65	1.71	92.3		0.24	3.9	2.88

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 (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	SEMET MODEL	1.65	38.69	16877	15839	845	98.89	0.21584	0.21372	0.21	0.25817	0.26	RANDOM	21.318

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]
0.05	0.03		0.05		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.876
r_dihedral_angle_4_deg	20.871
r_dihedral_angle_3_deg	14.328
r_dihedral_angle_1_deg	5.69
r_scangle_it	3.785
r_scbond_it	2.66
r_mcangle_it	1.713
r_angle_refined_deg	1.566
r_mcbond_it	1.087
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.212
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.099
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	868
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
CNS	refinement
CNS	phasing
d*TREK	data scaling