9W6S | pdb_00009w6s

hCA450-21.1 Fab and GD2 complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291.15	0.1 M HEPES sodium (pH 7.5), 1% (v/v) polyethylene glycol 400 (PEG 400), and 2.2 M ammonium

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.48	α = 90
b = 109.19	β = 90
c = 170.21	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 EIGER X 16M		2025-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97861	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.69	42.553	99.95	0.2	9	12.9		157524

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.69	1.734			0.293

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	THROUGHOUT	1.69	42.553	157524	8080	99.949	0.182	0.181	0.1829	0.2053	0.2075	23.268

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]
-0.838			1.414		-0.576

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.544
r_dihedral_angle_3_deg	11.949
r_dihedral_angle_2_deg	8.109
r_lrange_it	7.364
r_dihedral_angle_1_deg	7.294
r_lrange_other	7.288
r_scangle_it	5.249
r_scangle_other	5.248
r_mcangle_it	3.669
r_mcangle_other	3.668
r_scbond_it	3.466
r_scbond_other	3.466
r_mcbond_it	2.519
r_mcbond_other	2.519
r_angle_refined_deg	1.866
r_angle_other_deg	0.642
r_nbd_refined	0.22
r_symmetry_nbd_other	0.2
r_nbd_other	0.187
r_symmetry_nbd_refined	0.181
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.113
r_chiral_restr	0.093
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	6513
Nucleic Acid Atoms
Solvent Atoms	792
Heterogen Atoms	194

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing