5R8K | pdb_00005r8k

PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z355728146 in complex with INTERLEUKIN-1 BETA

X-RAY DIFFRACTION

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	61.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.71	α = 90
b = 54.71	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	1.47	37.56	100	0.049	0.053	0.02	0.999	17.6	6.6		37619

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	1.47	1.51	100		1.782	1.936	0.75	0.413		6.6	2785

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	1.47	34.42	35698	1886	99.95	0.1918	0.1909	0.24	0.2089	0.26	RANDOM	27.537

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]
-0.46			-0.46		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.725
r_dihedral_angle_3_deg	14.456
r_dihedral_angle_4_deg	10.975
r_dihedral_angle_1_deg	8.255
r_mcangle_it	4.255
r_mcbond_other	2.71
r_mcbond_it	2.692
r_angle_refined_deg	1.846
r_angle_other_deg	1.417
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.725
r_dihedral_angle_3_deg	14.456
r_dihedral_angle_4_deg	10.975
r_dihedral_angle_1_deg	8.255
r_mcangle_it	4.255
r_mcbond_other	2.71
r_mcbond_it	2.692
r_angle_refined_deg	1.846
r_angle_other_deg	1.417
r_chiral_restr	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1190
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	24

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.