3ERP | pdb_00003erp

Structure of IDP01002, a putative oxidoreductase from and essential gene of Salmonella typhimurium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZSX	PDB code 1ZSX was used for MR on a crystal diffracting to 2.15 A on our RAXIS4 home source. The protein atoms from the model refined from that crystal were used for rigid body refinement with the new data diffracting to 1.55 A.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	295	crystallized in 0.2 M Calcium Acetate, 9% PEG8000 and 0.1 M Sodium Cacodylate. Cryoprotected with 25% ethylene glycol., pH 6.5, EVAPORATION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.096	α = 90
b = 127.096	β = 90
c = 120.492	γ = 90

Symmetry
Space Group	I 4

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	MARMOSAIC 300 mm CCD	mirrors	2008-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.55	30	97.2	0.06	23.08	5.2	136598	132754			17.8

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	1.55	1.61	80.3		0.477	2.62	4.6	13638

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 code 1ZSX was used for MR on a crystal diffracting to 2.15 A on our RAXIS4 home source. The protein atoms from the model refined from that crystal were used for rigid body refinement with the new data diffracting to 1.55 A.	1.55	29.96	125986	6743	96.83	0.15465	0.15342	0.15	0.17771	0.18	RANDOM. R-free set for the second crystal was imported from the first crystal and extended to 1.55 A	23.404

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]
-1.03			-1.03		2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.256
r_dihedral_angle_4_deg	14.284
r_dihedral_angle_3_deg	11.137
r_scangle_it	5.191
r_dihedral_angle_1_deg	4.478
r_scbond_it	3.316
r_mcangle_it	2.137
r_angle_refined_deg	1.517
r_mcbond_it	1.309
r_chiral_restr	0.12
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	4920
Nucleic Acid Atoms
Solvent Atoms	844
Heterogen Atoms	71

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling