2C8Y

thrombin inhibitors

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QJ1	PDB ENTRY 1QJ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.3		PH 7.30

Crystal Properties
Matthews coefficient	Solvent content
2.38	47.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.731	α = 90
b = 71.516	β = 100.51
c = 72.422	γ = 90

Symmetry
Space Group	C 1 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	CCD	RIGAKU CCD	CONFOCAL MULTILAYER		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	2.2	29.22	99.7	0.13	5.3	2.91		18049

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	2.2	2.28	99.1		0.44	2.2	2.82

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 1QJ1	2.2	29.22	17132	916	99.7	0.188	0.185	0.259	RANDOM	26.73

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]
0.5		-1.52	-0.45		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.338
r_dihedral_angle_4_deg	17.283
r_dihedral_angle_3_deg	14.239
r_dihedral_angle_1_deg	6.375
r_angle_refined_deg	1.386
r_angle_other_deg	0.855
r_symmetry_vdw_other	0.258
r_nbd_refined	0.202
r_nbd_other	0.192
r_nbtor_refined	0.183
r_symmetry_hbond_refined	0.139
r_xyhbond_nbd_refined	0.106
r_scangle_it	0.099
r_chiral_restr	0.085
r_scbond_it	0.083
r_nbtor_other	0.082
r_mcangle_it	0.08
r_symmetry_vdw_refined	0.063
r_mcbond_it	0.058
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2362
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
IN-HOUSE	phasing