8PUK | pdb_00008puk

ChiLob 7/4 H2 HC-T219C/C224S Kappa LC-E123C/C214S F(ab')2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TKE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	294.15	0.1M TRIS, 15% PEG 4000, 0.2M (NH4)2SO4
2	VAPOR DIFFUSION, SITTING DROP	8	294.15	0.1M TRIS, 25% PEG 4000, 15% glycerol

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.167	α = 90
b = 148.167	β = 90
c = 45.295	γ = 120

Symmetry
Space Group	P 3 2 1

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 4M		2022-04-13	M	SINGLE WAVELENGTH
2	2	x-ray	45	PIXEL	DECTRIS PILATUS 12M		2022-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3
2	SYNCHROTRON	DIAMOND BEAMLINE I23	2.75	Diamond	I23

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	2.67	74.193	98.8	0.129	0.149	0.075	0.995	10.1	7.1		16178

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	2.67	2.8	97.1		1.725	1.995	0.986	0.384	0.9

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	2.671	74.193	16177	798	98.532	0.244	0.2422	0.2445	0.2825	0.2881	74.386

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]
2.787	1.393		2.787		-9.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.849
r_dihedral_angle_6_deg	13.535
r_dihedral_angle_1_deg	8.475
r_dihedral_angle_2_deg	7.159
r_lrange_it	4.227
r_lrange_other	4.226
r_mcangle_it	2.185
r_mcangle_other	2.185
r_scangle_it	2.161
r_scangle_other	2.115
r_scbond_it	1.388
r_scbond_other	1.356
r_mcbond_it	1.26
r_mcbond_other	1.259
r_angle_refined_deg	1.167
r_symmetry_xyhbond_nbd_refined	0.705
r_angle_other_deg	0.391
r_symmetry_nbd_refined	0.263
r_nbd_refined	0.202
r_symmetry_nbd_other	0.201
r_nbd_other	0.183
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.155
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.064
r_chiral_restr	0.051
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3284
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building
xia2	data reduction