1H8D | pdb_00001h8d

X-ray structure of the human alpha-thrombin complex with a tripeptide phosphonate inhibitor.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2		20% PEG 8K, 0.05MM NAHPO4, 0.1M NACL, PH 7.20

Crystal Properties
Matthews coefficient	Solvent content
2.59	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.64	α = 90
b = 71.6	β = 100.35
c = 71.9	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				1998-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX7.2		SRS	PX7.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.4	15	95.4	0.052	0.056	23	3		68615		5	16.27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	96.6		0.142	0.131	6	2

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1HGT	1.4	14	68615		95.4	0.17	0.18	0.22	0.22	18.5

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
p_angle_d	1.2
p_bond_d	0.008
p_angle_deg
p_planar_d
p_hb_or_metal_coord
p_mcbond_it
p_mcangle_it
p_scbond_it
p_scangle_it
p_plane_restr
p_chiral_restr
p_singtor_nbd
p_multtor_nbd
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2349
Nucleic Acid Atoms
Solvent Atoms	684
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing