Experiment: 5VH3

Crystal structure of Fab fragment of the anti-TNFa antibody infliximab in a C-centered orthorhombic crystal form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4G3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	Fab at 10 mg/mL against Wiz 34 screen condition B4 20% PEG 3350, 0.2 M potassium citrate tribasic supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 267664b4, unique puck ID sdw5-2

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.58	α = 90
b = 138.82	β = 90
c = 195.46	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	CCD	MARMOSAIC 300 mm CCD		2015-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	50	100	0.126	0.137	0.994	10.52	6.246		79590		-3	21.24

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	100		0.539	0.588	0.889	3.7	6.289

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4g3y	2	50	1.36	79576	3868	99.95	0.1617	0.1597	0.1607	0.1996	0.1999	27.218

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.08
f_angle_d	0.788
f_chiral_restr	0.053
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6515
Nucleic Acid Atoms
Solvent Atoms	1047
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XSCALE	data scaling
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing