7E61

The crystal structure of peptidoglycan peptidase in complex with inhibitor 2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		296	0.1 M sodium acetate: acetic acid pH 4.5 and 0.8 M NaH2PO4/1.2 M K2HPO4

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.175	α = 90
b = 115.175	β = 90
c = 55.34	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2020-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.9796	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.8	48.403	100	0.048	0.051	1	29.48	10.595		38961			35.238

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.91	100		0.541	0.568	0.945	4.33	10.84

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	6JMZ	1.8	48.403	37012	1948	99.98	0.1569	0.1554	0.1871	RANDOM	34.931

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.9
r_dihedral_angle_4_deg	16.584
r_dihedral_angle_3_deg	14.967
r_dihedral_angle_1_deg	6.395
r_angle_refined_deg	2.437
r_angle_other_deg	1.048
r_chiral_restr	0.161
r_bond_refined_d	0.026
r_gen_planes_refined	0.012
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.9
r_dihedral_angle_4_deg	16.584
r_dihedral_angle_3_deg	14.967
r_dihedral_angle_1_deg	6.395
r_angle_refined_deg	2.437
r_angle_other_deg	1.048
r_chiral_restr	0.161
r_bond_refined_d	0.026
r_gen_planes_refined	0.012
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2014
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	29

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	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 R01GM133198.