Experiment: 5KMW

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.1	293.15	30 microliters of 10 mg/ml protein concentration was added to a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1). For ligand soaking, crystals were placed for 2-3 h in a reservoir solution containing 2.7 M ammonium sulfate, 0.1 M sodium citrate (pH 6.1), and 5.0 mM benzyl penicillin. The crystals were then placed momentarily in a reservoir solution containing a cryoprotectant (30% w/v trehalose) and subsequently flash-frozen in liquid nitrogen

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.262	α = 90
b = 72.262	β = 90
c = 98.193	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	15	CCD	ADSC QUANTUM 315r		2015-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.67	APS	19-ID

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	1.1	38.62	99.7	0.093	5.6	5.5		118234

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	1.1	1.16	98.6		0.4	2.1	5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	FREE R	1.1	10		98.4	0.136		0.13	0.17	0.15	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
19		2443.8

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.4
s_approx_iso_adps	0.1587
s_anti_bump_dis_restr	0.0988
s_similar_adp_cmpnt	0.0436
s_bond_d	0.0147
s_from_restr_planes	0.005
s_angle_d
s_similar_dist
s_zero_chiral_vol
s_rigid_bond_adp_cmpnt

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2013
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms	94

Software

Software
Software Name	Purpose
SHELXL-97	refinement
XDS	data scaling
SCALA	data scaling
Coot	model building
SHELX	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.