3RFI

Crystal structure of the saposin-like domain of plant aspartic protease from Solanum tuberosum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Lithium sulfate monohydrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.47	α = 90
b = 56.47	β = 90
c = 55.34	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	100	IMAGE PLATE	MAR scanner 345 mm plate		2009-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.5418

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	1.9	40	99.9	0.059	24.1	10.3	8363	8355

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	1.9	2	100		0.9	2.87	10.3	1159

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	25	7936	417	100	0.18995	0.18697	0.2498	RANDOM	18.949

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.423
r_dihedral_angle_4_deg	34.286
r_dihedral_angle_3_deg	16.084
r_scangle_it	6.298
r_dihedral_angle_1_deg	4.703
r_scbond_it	3.807
r_mcangle_it	1.983
r_angle_refined_deg	1.808
r_mcbond_it	1.049
r_chiral_restr	0.146

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.423
r_dihedral_angle_4_deg	34.286
r_dihedral_angle_3_deg	16.084
r_scangle_it	6.298
r_dihedral_angle_1_deg	4.703
r_scbond_it	3.807
r_mcangle_it	1.983
r_angle_refined_deg	1.808
r_mcbond_it	1.049
r_chiral_restr	0.146
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	620
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.