Experiment: 7SIQ

Crystal structure of a peptide chain release factor 3 (prfC) from Stenotrophomonas maltophilia bound to GDP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TR5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	287	StmaA.18013.a.B1.PW38802 at 20.5 mg/mL with 3 mM MgCl2 and 3 mM GDP against Morpheus screen condition D5 containing 10% PEG 20,000, 20% PEG 550 MME, 0.02 mM each 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, 0.1 M MOPES/Hepes pH 7.5, direct cryo, unique puck ID tja6-9, crystal tracking ID 315959d5

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.54	α = 90
b = 96.54	β = 90
c = 170.07	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	287	CCD	RAYONIX MX-300		2020-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9787	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	2.95	48.27	99.8	0.068	0.071	0.999	22.82	10.855		19936			84.1

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	2.95	3.03	99.7		0.732	0.767	0.991	4	11.162

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	THROUGHOUT	3tr5	2.95	48.27	1.37	19688	945	98.82	0.2263	0.2235	0.2245	0.2786	0.2763	103.2994

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3866
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	28

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction