3B23 | pdb_00003b23

Crystal structure of thrombin-variegin complex: Insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	277	100mM HEPES buffer pH 7.4, 20-25% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.658	α = 90
b = 50.826	β = 98.7
c = 61.535	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	ADSC QUANTUM 315r		2007-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9795	NSLS	X29A

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	2.4	50	98.1	0.053	20	3.6		15137		-3

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	2.4	2.46	97		0.154	5.4	3.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ABI	2.4	30	13298	724	92.82	0.21049	0.20787	0.21	0.25944	0.24	RANDOM	57.826

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]
-1.05		-4.79	2.49		-2.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.426
r_dihedral_angle_4_deg	19.229
r_dihedral_angle_3_deg	14.327
r_dihedral_angle_1_deg	6.818
r_scangle_it	1.936
r_angle_refined_deg	1.224
r_scbond_it	1.191
r_mcangle_it	0.931
r_angle_other_deg	0.811
r_mcbond_it	0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.426
r_dihedral_angle_4_deg	19.229
r_dihedral_angle_3_deg	14.327
r_dihedral_angle_1_deg	6.818
r_scangle_it	1.936
r_angle_refined_deg	1.224
r_scbond_it	1.191
r_mcangle_it	0.931
r_angle_other_deg	0.811
r_mcbond_it	0.49
r_mcbond_other	0.078
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2464
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.