3QZM | pdb_00003qzm

Staphylococcus aureus IsdA NEAT domain H83A variant 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	2ITF	PDB ENTRY 2ITF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.2 M ammonium sulfate, 0.1 M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.49	α = 90
b = 51.76	β = 91.94
c = 55.69	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r	Sample to detector distance: 107 to 650 mm; Maximum vertical offset: 75mm	2010-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.0	SSRL	BL7-1

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	1.25	55.658	97.2	0.046	14.7	3.4	80164	80164			9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.32	87		0.141	0.141	5	2.5	10388

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 ENTRY 2ITF	1.25	55.658	80088	4026	97.06	0.1401	0.1388	0.1368	0.164	0.1611	RANDOM	12.5754

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]
-0.12		-0.52	-0.01		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.902
r_dihedral_angle_4_deg	20.873
r_dihedral_angle_3_deg	13.809
r_dihedral_angle_1_deg	7.02
r_scangle_it	5.036
r_scbond_it	3.559
r_mcangle_it	2.712
r_mcbond_it	1.696
r_angle_refined_deg	1.676
r_rigid_bond_restr	1.628
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2008
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	162

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOLREP	phasing