6ISL | pdb_00006isl

SnoaL-like cyclase XimE with its product xiamenmycin B

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	2M xiamenmycin B, 0.2M malonic acid, 20% PEG 3350, pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.22	α = 90
b = 80.22	β = 90
c = 112.2	γ = 120

Symmetry
Space Group	H 3

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 PILATUS3 6M		2017-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9778	SSRF	BL18U1

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	1.77	59.1	100	0.115	12.7	4.9		24399

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	1.77	1.8	100		0.515	3.3	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.77	59.07	24399	1243	97.56	0.1966	0.1953	0.2081	0.2205	0.2271	RANDOM	21.267

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]
-0.08	-0.04		-0.08		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.078
r_dihedral_angle_4_deg	17.727
r_dihedral_angle_3_deg	14.085
r_dihedral_angle_1_deg	7.175
r_angle_refined_deg	1.987
r_angle_other_deg	1.097
r_chiral_restr	0.122
r_bond_refined_d	0.02
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1858
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
PDB_EXTRACT	data extraction
HKL-3000	data scaling
MOLREP	phasing