1ORF

The Oligomeric Structure of Human Granzyme A Reveals the Molecular Determinants of Substrate Specificity

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	Tris pH 8.5, PEG 4000, lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.034	α = 90
b = 145.022	β = 90
c = 39.555	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC QUANTUM 4		2002-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	20	99.5			13319	12664

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	94.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1DST	2.4	20	13319	12664	660	99.46	0.19339	0.19137	0.19137	0.23245	RANDOM	35.985

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]
-1.98			2.91		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.345
r_scangle_it	3.433
r_scbond_it	2.039
r_angle_refined_deg	1.543
r_mcangle_it	1.39
r_mcbond_it	0.713
r_symmetry_vdw_refined	0.4
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.345
r_scangle_it	3.433
r_scbond_it	2.039
r_angle_refined_deg	1.543
r_mcangle_it	1.39
r_mcbond_it	0.713
r_symmetry_vdw_refined	0.4
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.105
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1774
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

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.