1W3M | pdb_00001w3m

Crystal structure of tsushimycin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4		0.1 M NAAC/HAC PH=4.0 0.12 M HAC 38% ETOH 0.80 M CACL2 0.40 M 1,6-HEXANEDIOL

Crystal Properties
Matthews coefficient	Solvent content
2.41	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.488	α = 65.64
b = 36.386	β = 68.35
c = 37.511	γ = 69.88

Symmetry
Space Group	P 1

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	MARRESEARCH	MIRRORS	2003-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	26.02	96.2	0.1	9.49	4.5		355145

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.1	92.1		0.5	3.35	3.62

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	DIRECT METHODS	FREE R-VALUE	1	99	75901	3848	96.2	0.1385	0.1374		0.1401	0.1711	THIN SHELLS

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
26	829	1259.82

RMS Deviations
Key	Refinement Restraint Deviation
s_from_restr_planes	0.428
s_non_zero_chiral_vol	0.117
s_zero_chiral_vol	0.09
s_approx_iso_adps	0.089
s_similar_adp_cmpnt	0.049
s_angle_d	0.033
s_bond_d	0.015
s_rigid_bond_adp_cmpnt	0.005
s_similar_dist
s_anti_bump_dis_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	924
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	161

Software

Software
Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling
SHELXD	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.