2FHH

Crystal Structure of Mycobacterium Tuberculosis Proteasome in complex with a peptidyl boronate inhibitor MLN-273

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q5Q	PDB ENTRY 1Q5Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	293	8% PEG 6000, 50 mM sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.957	α = 90
b = 116.172	β = 112.71
c = 200.203	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	77	CCD	ADSC QUANTUM 4		2005-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.0	NSLS	X25

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	2.99	50	0.944	0.058	18.6		398981	139848	2	2

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	2.99	3.11	0.844		0.25	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1Q5Q	2.99	50	2	139848	132804	7037	94.12	0.228	0.22814	0.22636	0.26163	RANDOM	85.398

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]
3.28		3.52	1.05		-1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.054
r_dihedral_angle_3_deg	21.075
r_dihedral_angle_4_deg	18.922
r_dihedral_angle_1_deg	4.857
r_scangle_it	1.69
r_angle_refined_deg	1.298
r_mcangle_it	1.006
r_scbond_it	0.949
r_mcbond_it	0.571
r_symmetry_vdw_refined	0.412

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.054
r_dihedral_angle_3_deg	21.075
r_dihedral_angle_4_deg	18.922
r_dihedral_angle_1_deg	4.857
r_scangle_it	1.69
r_angle_refined_deg	1.298
r_mcangle_it	1.006
r_scbond_it	0.949
r_mcbond_it	0.571
r_symmetry_vdw_refined	0.412
r_nbtor_refined	0.308
r_nbd_refined	0.241
r_symmetry_hbond_refined	0.231
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	46620
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	448

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
SCALEPACK	data scaling
CNS	phasing

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.