Experiment: 6CYM

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		294	For complex formation, 2 mg human alpha-thrombin (7.1 mg/mL in 50% v/v glycerol) were mixed with 0.5 mM Compound 1 in DMSO and dialyzed overnight into a solution of 20 mM sodium citrate and 1.3 mM Na2SO4 (pH 5.8). After dialysis, another 0.5 mM compound were added and left to incubate at room temperature for 1 h. The protein was centrifuged for 5 min at 4 deg C and 8000x RCF. The pellet, including about 120 uL of buffer, was mixed with 100 uL of a solution containing 50 mM sodium phosphate (pH 7.3), 190 mM sodium chloride, and 0.2 mM Compound 1. The crystal used for data collection was grown from the JCSG+ screen in well A10. The crystal was grown at 20 deg C using a MRC 3-well plate and in a 150 + 150 nL drop with a reservoir of 0.2 M potassium formate and 20% w/v PEG-3350.

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.67	α = 90
b = 99.73	β = 90
c = 146.01	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	PIXEL	DECTRIS PILATUS3 6M		2016-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.9	30	72.1	8.2	6.5		10936			73.56

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	2.9	2.95

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		THROUGHOUT	2.9	30	10936	566	72.1	0.18	0.176	0.254	RANDOM	69.84

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]
-5.9755			8.7076		-2.7322

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	22.45
t_omega_torsion	2.89
t_angle_deg	1.19
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	22.45
t_omega_torsion	2.89
t_angle_deg	1.19
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4556
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	36

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	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.