6X9X | pdb_00006x9x

Crystal structure of Fab fragment of Anti-HCV E2 antibody (HC84.26)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ESA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	0.4 M Ammonium Acetate, 20% PEG 2000 MME, Cryoprotectant-Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.535	α = 90
b = 113.699	β = 90
c = 122.696	γ = 90

Symmetry
Space Group	C 2 2 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		2019-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.979	APS	23-ID-B

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	1.8	50	99.8	0.053	0.059	0.025	0.996	26.41	5.1		53599			28.44

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	1.8	1.86	99.9		0.649	0.728	0.326	0.771	2.18	4.8

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	5ESA	1.8	34.9	50913	2648	99.68	0.17993	0.17839	0.19	0.20966	0.22	RANDOM	41.292

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]
-0.35			-0.31		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.461
r_dihedral_angle_4_deg	21.404
r_dihedral_angle_1_deg	18.673
r_dihedral_angle_3_deg	12.097
r_long_range_B_refined	7.926
r_long_range_B_other	7.864
r_scangle_other	5.061
r_mcangle_it	3.795
r_mcangle_other	3.795
r_scbond_other	3.337
r_scbond_it	3.336
r_mcbond_it	2.429
r_mcbond_other	2.428
r_angle_refined_deg	1.472
r_angle_other_deg	1.072
r_chiral_restr	0.089
r_bond_refined_d	0.012
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	3184
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
PHASER	phasing