5JW5 | pdb_00005jw5

Structure of MEDI8852 Fab Fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HOT	3HOT (chain B) 4KMT (chain L)
experimental model	PDB	4KMT	3HOT (chain B) 4KMT (chain L)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG3350, 0.2 M Ammonium Dihydrogen Phosphate, seeded from crystals obtained from 18% PEG8000, 0.1 M Sodium Cacodylate pH 6.5 and 0.2 M Calcium Acetate

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.22	α = 90
b = 109.92	β = 90
c = 139.89	γ = 90

Symmetry
Space Group	P 21 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 PILATUS3 6M		2014-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97941	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	86.43	97.3	0.098	0.995	10	4.1		77785		-3	31.51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	98.4		0.745	2.41

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	3HOT (chain B) 4KMT (chain L)	1.9	86.43	73943	3842	97.26	0.188	0.1866	0.19	0.2171	0.22	RANDOM	29.378

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]
-0.6			1.5		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.471
r_dihedral_angle_4_deg	18.436
r_dihedral_angle_3_deg	12.563
r_dihedral_angle_1_deg	6.623
r_mcangle_it	2.534
r_mcbond_it	1.721
r_mcbond_other	1.701
r_angle_refined_deg	1.53
r_angle_other_deg	1.157
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6548
Nucleic Acid Atoms
Solvent Atoms	559
Heterogen Atoms	15

Software

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