3HX9

Structure of heme-degrader, MhuD (Rv3592), from Mycobacterium tuberculosis with two hemes bound in its active site

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	0.1 M Bis-Tris pH 5.0, 0.2 M NaCl, 20% PEG-3350, 10 mM triethylamine HCl , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.971	α = 90
b = 64.622	β = 90.01
c = 71.082	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	70	CCD	ADSC QUANTUM 315r	Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).	2008-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97, 1.76	SSRL	BL7-1

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	1.75	50	98.9	0.066	28.1			19968

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)
	1.75	1.81	98.6		0.165	10.7		1974

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.75	19.35	18936	1018	98.87	0.18856	0.18623	0.23119	RANDOM	22.804

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]
-0.37		0.01	0.11		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.265
r_dihedral_angle_4_deg	16.771
r_dihedral_angle_3_deg	15.313
r_dihedral_angle_1_deg	6.629
r_scangle_it	5.586
r_scbond_it	3.649
r_mcangle_it	2.435
r_angle_refined_deg	2.01
r_mcbond_it	1.382
r_chiral_restr	0.161

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.265
r_dihedral_angle_4_deg	16.771
r_dihedral_angle_3_deg	15.313
r_dihedral_angle_1_deg	6.629
r_scangle_it	5.586
r_scbond_it	3.649
r_mcangle_it	2.435
r_angle_refined_deg	2.01
r_mcbond_it	1.382
r_chiral_restr	0.161
r_bond_refined_d	0.022
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1496
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	174

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.