9KHC | pdb_00009khc

Crystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule) complexed with GPRP peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FIB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	The reservoir solution contains 0.1 M MES pH 6.0, 20% PEG8000, and 70 mM CaCl2. After clystals were grown, the reservoir solution containing 20 mM GPRP was added to the drop.

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.897	α = 90
b = 66.947	β = 98.29
c = 91.428	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS EIGER X 16M	Focusing Mirror	2024-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.32	45.24	97.7	0.081	0.088	0.033	0.999	14.9	6.9		100678			11.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.32	1.34			1.07	1.16	0.442	0.63	2	6.7

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	1.32	45.24	100641	5054	97.484	0.171	0.1694	0.1694	0.2033	0.2034	RANDOM	18.756

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]
-0.934		-0.094	1.948		-0.946

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.467
r_dihedral_angle_3_deg	12.132
r_lrange_it	11.746
r_dihedral_angle_1_deg	6.719
r_scangle_it	5.88
r_mcangle_it	5.661
r_dihedral_angle_2_deg	5.488
r_scbond_it	3.793
r_mcbond_it	3.577
r_rigid_bond_restr	3.011
r_angle_refined_deg	1.355
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.229
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.121
r_chiral_restr	0.083
r_metal_ion_refined	0.074
r_gen_planes_refined	0.007
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4034
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	14

Software

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