2ZKS

Structural insights into the proteolytic machinery of apoptosis-inducing Granzyme M

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	20% PEG3350, 0.2M Li2SO4, 0.1M Bicine, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.671	α = 90
b = 74.671	β = 90
c = 113.557	γ = 120

Symmetry
Space Group	P 31 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	93	FLAT PANEL	MARRESEARCH Flat Panel		2008-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BSRF BEAMLINE 1W2B	0.9789	BSRF	1W2B

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	2.7	64.68	95.04	0.094	7.3		10499	9978

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 2GZC	2.7	56.19	9978	501	99.83	0.22609	0.22279	0.29308	RANDOM	30.385

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]
-0.17	-0.09		-0.17		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.365
r_dihedral_angle_4_deg	21.018
r_dihedral_angle_3_deg	17.656
r_dihedral_angle_1_deg	7.377
r_scangle_it	3.219
r_scbond_it	2.018
r_angle_refined_deg	1.88
r_mcangle_it	1.348
r_mcbond_it	0.775
r_symmetry_vdw_refined	0.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.365
r_dihedral_angle_4_deg	21.018
r_dihedral_angle_3_deg	17.656
r_dihedral_angle_1_deg	7.377
r_scangle_it	3.219
r_scbond_it	2.018
r_angle_refined_deg	1.88
r_mcangle_it	1.348
r_mcbond_it	0.775
r_symmetry_vdw_refined	0.328
r_nbtor_refined	0.32
r_symmetry_hbond_refined	0.275
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1783
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASES	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.