4G6M | pdb_00004g6m

Crystal structure of human IL-1beta in complex with therapeutic antibody binding fragment of gevokizumab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PZ5	1PZ5, 3BKJ, 1TOO
experimental model	PDB	3BKJ	1PZ5, 3BKJ, 1TOO
experimental model	PDB	1TOO	1PZ5, 3BKJ, 1TOO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5	293	20% w/v PEG 4000, 0.2M ammonium formate supplemented with 10% w/v polyvinylpyrrolidone K15, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.884	α = 90
b = 73.651	β = 90
c = 111.254	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	PSI PILATUS 6M		2012-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	111.3	99.7	0.085	0.093	14.6	5.5		51619		2	25.54

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	100		14.6	5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1PZ5, 3BKJ, 1TOO	1.81	26.5	51619	50918	2589	98.8	0.203	0.202	0.19	0.226	0.22	RANDOM	31.09

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]
-4.713			1.5524		3.1607

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.01
t_omega_torsion	2.89
t_angle_deg	1.02
t_bond_d	0.007
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4501
Nucleic Acid Atoms
Solvent Atoms	442
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data scaling
autoPROC	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
SCALA	data scaling