6P4C | pdb_00006p4c

HyHEL10 Fab carrying four heavy chain mutations (HyHEL10-4x): L4F, Y33H, S56N, and Y58F

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D9A	PDB entry 3D9A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	100 mM citrate, pH 4.2, 1 M lithium chloride, 11% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.556	α = 90
b = 40.156	β = 107.57
c = 93.649	γ = 90

Symmetry
Space Group	P 1 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 16M		2019-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	1.85	46.47	100	0.051	0.056	0.022	0.999	16.8	6.6		42030

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	1.85	1.89	100		0.862	0.947	0.386	0.778		6

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 (Observed)	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	PDB entry 3D9A	1.85	46.47	39937	2089	99.88	0.1898	0.188	0.1949	0.2229	0.2291	RANDOM	38.431

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]
-1.26		0.27	2.55		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.393
r_dihedral_angle_4_deg	25.389
r_dihedral_angle_3_deg	15.267
r_dihedral_angle_1_deg	7.593
r_angle_refined_deg	1.783
r_angle_other_deg	1.424
r_chiral_restr	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3150
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	7

Software

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