3RTL | pdb_00003rtl

Staphylococcus aureus heme-bound IsdB-N2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Selenomethionine-labeled IsdB-N2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	0.1 M Tris, 25% PEG 3350, 0.1 M MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.527	α = 90
b = 82.608	β = 90
c = 116.888	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 325 mm CCD	Rh coated flat mirror; toroidal focusing mirror	2009-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.0	SSRL	BL9-2

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	1.453	67.42	99.4	0.05	21.7	7.1		97666

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	1.453	1.5	95.2		0.373		5.7	9250

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	Selenomethionine-labeled IsdB-N2	1.453	67.42	97572	4876	98.86	0.1799	0.178	0.1759	0.2168	0.2134	RANDOM	20.6395

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]
-0.69			0.27		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.477
r_dihedral_angle_4_deg	19.244
r_dihedral_angle_3_deg	14.355
r_dihedral_angle_1_deg	6.601
r_sphericity_free	6.368
r_sphericity_bonded	4.342
r_scangle_it	3.823
r_scbond_it	2.632
r_mcangle_it	2.022
r_rigid_bond_restr	1.487
r_angle_refined_deg	1.379
r_mcbond_it	1.232
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3866
Nucleic Acid Atoms
Solvent Atoms	623
Heterogen Atoms	178

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection