5R87 | pdb_00005r87

PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z44592329 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
3.22	61.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.65	α = 90
b = 54.65	β = 90
c = 75.05	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	44.18	99.6	0.05	0.054	0.021	0.998	16.6	6.6		37383

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	99.8		1.611	1.747	0.672	0.468		6.6	2777

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	44.22	35465	1877	99.56	0.1961	0.1953	0.26	0.2128	0.28	RANDOM	30.82

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]
-0.47			-0.47		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.445
r_dihedral_angle_3_deg	14.715
r_dihedral_angle_4_deg	9.082
r_dihedral_angle_1_deg	8.419
r_mcangle_it	4.196
r_mcbond_other	2.35
r_mcbond_it	2.339
r_angle_refined_deg	1.788
r_angle_other_deg	1.368
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.445
r_dihedral_angle_3_deg	14.715
r_dihedral_angle_4_deg	9.082
r_dihedral_angle_1_deg	8.419
r_mcangle_it	4.196
r_mcbond_other	2.35
r_mcbond_it	2.339
r_angle_refined_deg	1.788
r_angle_other_deg	1.368
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1194
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	26

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.