3VXF

X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	298	THE CRYSTAL WAS OBTAINED BY A SITTING DROP VAPOR DIFFUSION AFTER MACROSEEDING. 2% (W/V) TO 10% (W/V) PEG4000, 100MM SODIUM ACETATE PD5.0. THE INITIAL CONCENTRATION OF THROMBIN-BIVALIRUDIN COMPLEX WAS 5MG/ML, pH 5.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.998	α = 90
b = 107.8	β = 90
c = 45.888	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	ADSC QUANTUM 4r	Bending magnet, monochromator, mirrors	2009-06-13	M	SINGLE WAVELENGTH
2	2	neutron	298	IMAGE PLATE	BIX-4	monochromator	2009-03-23	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	1.0	Photon Factory	BL-6A
2	NUCLEAR REACTOR	JRR-3M BEAMLINE 1G-C	2.6	JRR-3M	1G-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.6	50	95.6	0.051						34.5		51182	51182		-3
2	2.8	100	80	0.134						4.79			8509			20.03

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66		0.332						5.2
1	1.66	1.72		0.243						6.8
1	1.72	1.8		0.173						10.9
1	1.8	1.9		0.125						13.8
1	1.9	2.02		0.088						17.9
1	2.02	2.17		0.068						22.7
1	2.17	2.39		0.056						29.1
1	2.39	2.74		0.047						39.7
1	2.74	3.45		0.04						44.9
1	3.45	50		0.036						45.6
2	2.8	2.9		0.33						1.81

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		1.602	29.227		1.35	51136	51136	1902	95.32		0.1619	0.1609	0.1555	0.1842	0.1793		17.899
NEUTRON DIFFRACTION		2.752	44.873				8072	404	73.72		0.1855	0.1828		0.2339			15.603

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]
-1.0167			2.9256		-1.9089
0.7967			-2.7111		1.9144

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.995
f_angle_d	2.044
f_chiral_restr	0.117
f_bond_d	0.016
f_plane_restr	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2357
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	14

Software

Software
Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.