6WI6 | pdb_00006wi6

Crystal structure of plantacyclin B21AG

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	1.1 M sodium malonate, 0.1 M HEPES pH7.0 and 0.5% v/v JED-2003

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.131	α = 90
b = 93.17	β = 90
c = 49.493	γ = 90

Symmetry
Space Group	C 2 2 21

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 EIGER X 16M		2017-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	1.8	46.58	99.8	0.076	0.079	0.022	0.999	15.5	13.1		9770

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	1.8	1.84	96.7		0.762	0.795	0.223	0.9		12.3

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	AB INITIO PHASING	THROUGHOUT	1.8	46.58	8753	993	99.83	0.1739	0.1693	0.1825	0.2152	0.2185	RANDOM	26.503

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]
0.94			-0.42		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	31.947
r_dihedral_angle_2_deg	26.382
r_dihedral_angle_3_deg	11.655
r_dihedral_angle_1_deg	5.437
r_angle_refined_deg	1.697
r_angle_other_deg	1.058
r_chiral_restr	0.103
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	802
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing
ARP/wARP	model building