2OBY | pdb_00002oby

Crystal structure of Human P53 inducible oxidoreductase (TP53I3,PIG3)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J8Z	PDB ENTRY 2J8Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	30 % PEG 4000, 0.1 M Tris, 0.2 M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.354	α = 90
b = 184.359	β = 90
c = 318.047	γ = 90

Symmetry
Space Group	C 2 2 21

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	MAR scanner 300 mm plate	Mirrors	2005-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	19.94	88.7			36209	36209			45.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.2	62.5

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 2J8Z	3	19.94	34254	34254	1795	88.63	0.22155	0.22155	0.21955	0.22	0.25968	0.26	RANDOM	40.61

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]
0.65			0.57		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.838
r_dihedral_angle_3_deg	13.798
r_dihedral_angle_4_deg	12.741
r_dihedral_angle_1_deg	5.169
r_angle_refined_deg	0.935
r_angle_other_deg	0.783
r_scangle_it	0.251
r_nbd_refined	0.183
r_nbtor_refined	0.166
r_scbond_it	0.164
r_nbd_other	0.162
r_symmetry_vdw_other	0.152
r_symmetry_hbond_refined	0.144
r_symmetry_vdw_refined	0.143
r_xyhbond_nbd_refined	0.119
r_mcangle_it	0.091
r_nbtor_other	0.08
r_mcbond_it	0.069
r_chiral_restr	0.049
r_mcbond_other	0.016
r_bond_refined_d	0.005
r_bond_other_d	0.004
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12580
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	240

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing