Experiment: 7U4H

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JCH	MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B
experimental model	PDB	5U2G	MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B
experimental model	PDB	3VMA	MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B
experimental model	PDB	4OON	MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	287	RigakuReagents Wizard3/4 screen condition B8: 100mM HEPES/NaOH pH 7.0, 10% (w/V) PEG 8000: ChtrB.19241.a.D11.PD228392 at 15.5mg/ml + 1mM imipenem: tray: 313782 b8: cryo: 25% EG: puck HIO1-1.

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.79	α = 90
b = 175.79	β = 90
c = 339.7	γ = 120

Symmetry
Space Group	H 3 2

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	RAYONIX MX-300	Beryllium Lenses	2020-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	3.1	50	99.8	0.112	0.128	0.995	11.77	4.35		36840			49.068

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	3.1	3.18	100		0.58	0.658	0.82	2.95	4.437

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B	3.1	47.6	1.35	36832	2016	99.8	0.1936	0.1923	0.19	0.2159	0.22	61.92

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
f_dihedral_angle_d	12.9451
f_angle_d	0.557
f_chiral_restr	0.0452
f_plane_restr	0.0041
f_bond_d	0.0027

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8883
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	50

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	phasing
Coot	model building

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.