9KHB | pdb_00009khb

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

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	Reservoir solution (22% PEG 8000, 150 mM 2-Morpholinoethanesulfonic acid, pH 6.0, 70 mM calcium choride) Protein solution (20 mM 2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonic acid, pH7.4, 120 mM sodium choride, 70 mM calcium choride)

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.797	α = 90
b = 66.656	β = 105.177
c = 46.564	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	2023-12-16	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	1.03	44.94	97.4	0.049	0.054	0.021	0.999	17.4	6.6		103954			10.6

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	1.03	1.05	93.3		0.714	0.776	0.298	0.828	2.2	6.6

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	1.03	44.94	103922	5116	97.254	0.12	0.1193	0.1194	0.1388	0.1388	13.445

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]
-0.395		-0.196	0.84		-0.295

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.12
r_dihedral_angle_3_deg	12.215
r_lrange_it	9.045
r_lrange_other	8.235
r_dihedral_angle_2_deg	6.711
r_dihedral_angle_1_deg	6.657
r_scangle_it	5.52
r_scangle_other	5.519
r_mcangle_other	4.069
r_mcangle_it	4.066
r_scbond_it	3.813
r_scbond_other	3.812
r_rigid_bond_restr	3.152
r_mcbond_it	2.794
r_mcbond_other	2.772
r_angle_refined_deg	1.691
r_angle_other_deg	0.65
r_nbd_other	0.206
r_nbd_refined	0.204
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.19
r_symmetry_nbd_refined	0.165
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2002
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	19

Software

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