9T00 | pdb_00009t00

Crystal structure of prethrombin-2 with a peptide corresponding to the C-terminus of the heavy chain of factor Va

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		Prethrombin-2 and peptide sequences provided

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	0.2 M NaCl (Salt) 0.1 M TRIS 8.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.416	α = 82.9
b = 51.567	β = 85.326
c = 65.992	γ = 65.901

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER2 XE 16M		2025-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.7838	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.8	38.76	99.2	0.244	0.95	3	3.7		15006

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	98.9		1.032	0.432	0.7	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.8	38.76	14980	719	99.074	0.261	0.2587	0.2644	0.3045	0.3064	RANDOM	47.074

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]
-3.825	2.451	-0.426	-1.163	-2.27	6.939

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.18
r_dihedral_angle_6_deg	9.479
r_dihedral_angle_1_deg	6.001
r_dihedral_angle_2_deg	5.187
r_lrange_it	4.517
r_lrange_other	4.517
r_mcangle_it	2.387
r_mcangle_other	2.387
r_scangle_it	1.64
r_scangle_other	1.64
r_mcbond_it	1.295
r_mcbond_other	1.295
r_scbond_it	0.85
r_scbond_other	0.85
r_angle_refined_deg	0.785
r_angle_other_deg	0.266
r_nbd_other	0.262
r_symmetry_nbd_refined	0.255
r_xyhbond_nbd_refined	0.251
r_symmetry_nbd_other	0.24
r_nbd_refined	0.228
r_symmetry_xyhbond_nbd_refined	0.214
r_nbtor_refined	0.187
r_ncsr_local_group_2	0.138
r_ncsr_local_group_1	0.114
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.05
r_symmetry_xyhbond_nbd_other	0.007
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5114
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing