4XS0 | pdb_00004xs0

Human methemoglobin in complex with the second and third NEAT domains of IsdH(F365Y/A369F/Y642A) from Staphylococcus aureus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IJ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	0.2 M K/Na tartrate, 0.1 M tri-sodium citrate pH 5.6, 2 M ammonium sulfate. Cryoprotected in 20% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.219	α = 90
b = 92.219	β = 90
c = 365.116	γ = 120

Symmetry
Space Group	P 65 2 2

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 210r		2013-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.96580	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.55	33.39	99.9	0.138	0.042	0.996	9.3	9.6		31237

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.66	100		0.825	0.252	0.766	2	9.7	3709

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	4IJ2	2.55	33.39	29544	1581	99.72	0.2608	0.2594	0.26	0.2871	0.29	RANDOM	67.181

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]
0.79	0.4		0.79		-2.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.127
r_dihedral_angle_4_deg	12.169
r_dihedral_angle_3_deg	11.847
r_dihedral_angle_1_deg	4.735
r_mcangle_it	2.32
r_mcbond_other	1.368
r_mcbond_it	1.367
r_angle_refined_deg	0.789
r_angle_other_deg	0.642
r_chiral_restr	0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.127
r_dihedral_angle_4_deg	12.169
r_dihedral_angle_3_deg	11.847
r_dihedral_angle_1_deg	4.735
r_mcangle_it	2.32
r_mcbond_other	1.368
r_mcbond_it	1.367
r_angle_refined_deg	0.789
r_angle_other_deg	0.642
r_chiral_restr	0.047
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4771
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.