9I24 | pdb_00009i24

Coagulation factor Xa complex with a2-loop peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IIT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		287	imidazole, MPD

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.473	α = 90
b = 72.419	β = 90
c = 82.335	γ = 90

Symmetry
Space Group	P 21 21 21

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		2024-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.70979	Diamond	I04

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	1.2	54.38	98.1	0.069	0.998	14.3	13.7		89301

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	96.5		0.633	0.672	1.3	14.4

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.2	54.378	89240	4536	97.832	0.143	0.1413	0.1493	0.1718	0.173	17.469

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]
-0.834			0.851		-0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.306
r_lrange_other	15.304
r_dihedral_angle_6_deg	14.886
r_dihedral_angle_2_deg	12.079
r_dihedral_angle_3_deg	11.676
r_scangle_it	10.601
r_scangle_other	10.598
r_mcangle_it	8.127
r_mcangle_other	8.125
r_scbond_it	7.564
r_scbond_other	7.561
r_dihedral_angle_1_deg	6.652
r_mcbond_it	5.816
r_mcbond_other	5.815
r_rigid_bond_restr	4.06
r_angle_refined_deg	1.977
r_angle_other_deg	0.731
r_dihedral_angle_other_2_deg	0.728
r_nbd_refined	0.319
r_xyhbond_nbd_refined	0.288
r_symmetry_nbd_refined	0.284
r_symmetry_nbd_other	0.228
r_nbd_other	0.211
r_symmetry_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_other	0.149
r_metal_ion_refined	0.121
r_chiral_restr	0.108
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2209
Nucleic Acid Atoms
Solvent Atoms	295
Heterogen Atoms	73

Software

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