5R86 | pdb_00005r86

PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z943693514 in complex with INTERLEUKIN-1 BETA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NVH	2NVH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.9	291	2.8M ammonium sulphate, 0.1M Tris pH7.9

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.67	α = 90
b = 54.67	β = 90
c = 75.11	γ = 90

Symmetry
Space Group	P 43

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 PILATUS 6M		2019-07-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96871	Diamond	I24

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	1.5	37.56	99.9	0.05	0.054	0.021	0.999	16.8	6.6		35360

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	1.5	1.54	100		1.443	1.565	0.6	0.508		6.6	2609

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	FOURIER SYNTHESIS	THROUGHOUT	2NVH	1.5	34.4	33546	1778	99.89	0.1938	0.1925	0.23	0.2189	0.24	RANDOM	32.442

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]
-0.41			-0.41		0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.151
r_dihedral_angle_3_deg	14.57
r_dihedral_angle_1_deg	8
r_dihedral_angle_4_deg	7.05
r_mcangle_it	5.231
r_mcbond_other	2.863
r_mcbond_it	2.84
r_angle_refined_deg	1.808
r_angle_other_deg	1.382
r_chiral_restr	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1170
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	23

Software

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