1S3R | pdb_00001s3r

Crystal structure of the human-specific toxin intermedilysin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	PEG 8000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.45	α = 90
b = 173.64	β = 90
c = 105.11	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2002-07-14	M	SINGLE WAVELENGTH
2	1	100	IMAGE PLATE	MARRESEARCH	mirrors	2002-04-23

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C
2	ROTATING ANODE	RIGAKU	1.54

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	2.5	30	99.2	0.047	0.047	37.7	6	50420	50420			81.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	97.6		0.368	0.368	4.5	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MIR	THROUGHOUT	2.6	30	50420	47850	2570	99.83	0.265	0.23233	0.22901	0.24	0.2951	0.31	RANDOM	35.356

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]
12.99			-9.54		-3.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.113
r_scangle_it	2.943
r_scbond_it	1.844
r_angle_refined_deg	1.582
r_mcangle_it	1.301
r_angle_other_deg	0.905
r_mcbond_it	0.721
r_nbd_other	0.251
r_symmetry_vdw_other	0.251
r_nbd_refined	0.23
r_symmetry_hbond_refined	0.227
r_xyhbond_nbd_refined	0.19
r_symmetry_vdw_refined	0.134
r_nbtor_other	0.091
r_chiral_restr	0.09
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7356
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing