5GDS | pdb_00005gds

HIRUNORMS ARE TRUE HIRUDIN MIMETICS. THE CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN:HIRUNORM V COMPLEX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HAH	PDB ENTRY 1HAH (J. VIJAYALAKSHMI ET AL., 1994, PROTEIN SCI. 3,2254-71)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	277	THE CRYSTALS OF THROMBIN:HIRUNORM V COMPLEX WERE GROWN, AS DESCRIBED BY SKRZYPEZAK ET AL. (1991) J. MOL. BIOL.,221,1379-1393 BY VAPOR DIFFUSION METHODS AT 4 C. A 6 MICROLITER DROP, CONTAINING 0.05 M SODIUM HEPES (PH 7.0) 10% (W/V) PEG 4000 0.02% NAN3, 20 MG/ML. THROMBIN:HIRUNORM V COMPLEX WAS EQUILIBRATED AGAINST A PRECIPITATING SOLUTION CONTAINING 0.1 M SODIUM HEPES (PH 7.0) 20% (W/V) PEG 4000 0.04% NAN3. CRYSTAL OF THROMBIN:HIRUGEN COMPLEX WERE CRUSHED AND INDIVIDUAL SEEDS WERE USED FOR CROSS-SEEDING EXPERIMENTS., vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.9	α = 90
b = 72.8	β = 100.7
c = 73.3	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	293	IMAGE PLATE	RIGAKU RAXIS II	COLLIMATOR	1996-01-10	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

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	2.1	20	99.4	0.072	5.8	2.5		21615			28.7

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	2.1	2.17	98.7		0.38	2	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	THE STRUCTURE WAS ANALYZED BY DIFFERENCE FOURIER TECHNIQUES	PDB ENTRY 1HAH (J. VIJAYALAKSHMI ET AL., 1994, PROTEIN SCI. 3,2254-71)	2.1	20	21609	21609		97	0.176	0.18

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]

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	17.835
t_angle_deg	2.8
t_nbd	0.23
t_trig_c_planes	0.021
t_gen_planes	0.021
t_bond_d	0.018
t_incorr_chiral_ct
t_pseud_angle
t_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2476
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	14

Software

Software
Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
CCP4	model building
TNT	refinement
CCP4	data scaling
CCP4	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.