5YOH

Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105M mutant) in complex with Methionine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1M Hepes, 27% Peg3350, 3% glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.332	α = 90
b = 48.69	β = 95.3
c = 56.151	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	IMAGE PLATE	RIGAKU RAXIS IV++		2016-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.62	28.59	92.2	0.027	0.038	0.026	0.998	59.8	1.9		32311			21.95

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.62	1.68	78.1		0.118	0.166	0.117	0.961		1.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1YJ3	1.63	28.59	32306	1526	96.89	0.1683	0.166	0.218	RANDOM	23.683

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.804
r_dihedral_angle_4_deg	21.046
r_dihedral_angle_3_deg	12.756
r_dihedral_angle_1_deg	6.198
r_angle_refined_deg	2.159
r_angle_other_deg	1.094
r_chiral_restr	0.132
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.804
r_dihedral_angle_4_deg	21.046
r_dihedral_angle_3_deg	12.756
r_dihedral_angle_1_deg	6.198
r_angle_refined_deg	2.159
r_angle_other_deg	1.094
r_chiral_restr	0.132
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2154
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	18

Software

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

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.