1XW4 | pdb_00001xw4

Crystal Structure of Human Sulfiredoxin (Srx) in Complex with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XW3	PDB ENTRY 1XW3

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.9	56.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.451	α = 90
b = 68.451	β = 90
c = 50.891	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	IMAGE PLATE	RIGAKU	CONFOCAL BLUE MAX-FLUX	2004-07-09	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	2	29.64	99.6	0.051	30.9	9.63		9562

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	95.3		4.4	5.03

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	PDB ENTRY 1XW3	2	29.6	9602	9084	456	99.43	0.22068	0.21825	0.22	0.27084	0.27	RANDOM	27.872

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]
0.54	0.27		0.54		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.158
r_dihedral_angle_4_deg	14.855
r_dihedral_angle_3_deg	14.42
r_dihedral_angle_1_deg	6.479
r_scangle_it	4.357
r_scbond_it	2.778
r_mcangle_it	1.834
r_angle_refined_deg	1.828
r_mcbond_it	1.126
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.24
r_xyhbond_nbd_refined	0.224
r_nbd_refined	0.216
r_chiral_restr	0.115
r_symmetry_hbond_refined	0.108
r_bond_refined_d	0.02
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	840
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	27

Software

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