8BBH | pdb_00008bbh

The crystal structure of a mouse Fab fragment TL1 in complex with a human Glucose-6-phosphate isomerase peptide 293-307

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		300	0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.66	α = 90
b = 75.545	β = 90
c = 96.219	γ = 90

Symmetry
Space Group	P 2 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		2020-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.97625	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.619	55.408	100	0.999	12.4	13.1		63532

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.62	8.87			0.666

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	model structure	1.619	55.408	63532	3038	99.994	0.199	0.1976	0.21	0.2291	0.24	25.727

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]
-0.017			0.028		-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18
r_dihedral_angle_2_deg	15.298
r_dihedral_angle_3_deg	14.465
r_lrange_it	7.371
r_lrange_other	7.313
r_dihedral_angle_1_deg	7.285
r_scangle_it	5.838
r_scangle_other	5.837
r_scbond_it	3.915
r_scbond_other	3.914
r_mcangle_it	3.3
r_mcangle_other	3.299
r_mcbond_it	2.3
r_mcbond_other	2.3
r_angle_refined_deg	1.602
r_angle_other_deg	0.555
r_symmetry_nbd_refined	0.476
r_nbd_other	0.323
r_nbd_refined	0.3
r_symmetry_xyhbond_nbd_refined	0.291
r_symmetry_nbd_other	0.222
r_xyhbond_nbd_refined	0.202
r_nbtor_refined	0.176
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.076
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3345
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling