4Z7M | pdb_00004z7m

Novel Inhibitors of Bacterial Methionine Aminopeptidase with Broad-Spectrum Biochemical Activity

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8		100 mM MES, 1.1 M ammonium sulfate, 0.1 M potassium chloride, 9% trehalose

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.985	α = 90
b = 62.712	β = 89.59
c = 72.978	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	MARMOSAIC 300 mm CCD		2014-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.000	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.43	47.57	92.1	4.3	6		71302

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.43	47.57	67700	3601	69.57	0.2539	0.2511	0.26	0.3055	0.31	RANDOM	32.034

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]
2.25		1.14	-3.26		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.883
r_dihedral_angle_4_deg	17.992
r_dihedral_angle_3_deg	14.592
r_dihedral_angle_1_deg	6.773
r_mcangle_it	3.011
r_mcbond_it	2.279
r_mcbond_other	2.279
r_angle_refined_deg	1.863
r_angle_other_deg	1.046
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.883
r_dihedral_angle_4_deg	17.992
r_dihedral_angle_3_deg	14.592
r_dihedral_angle_1_deg	6.773
r_mcangle_it	3.011
r_mcbond_it	2.279
r_mcbond_other	2.279
r_angle_refined_deg	1.863
r_angle_other_deg	1.046
r_chiral_restr	0.107
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4052
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
SCALA	data scaling
AMoRE	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.