3LGM | pdb_00003lgm

Crystal structure of reduced IsdI in complex with heme

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	25% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Bis-Tris buffer pH 5.5, and soaked in 50mM sodium dithionite for 10 minutes with a cryoprotectant of 10% ethylene glycol before freezing, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.04	α = 90
b = 68.03	β = 90
c = 70.75	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARMOSAIC 300 mm CCD	DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror.	2008-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97934	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.88	70.75	99.8	0.094		7	23396	23396

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 2ZDP	1.88	44.87	23423	23323	1195	99.68	0.221	0.203	0.2	0.2013	0.242	0.2409	RANDOM	29.569

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]
-1.46			-0.54		2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.601
r_dihedral_angle_3_deg	12.504
r_dihedral_angle_4_deg	11.566
r_dihedral_angle_1_deg	5.726
r_scangle_it	3.507
r_scbond_it	2.183
r_mcangle_it	1.534
r_angle_refined_deg	1.348
r_mcbond_it	0.811
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1845
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	87

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction