8ABT

Crystal structure of NaLdpA in complex with the product analog Resveratrol

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	2 M ammonium sulfate, 2% PEG 400, 0.1 M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.045	α = 90
b = 78.045	β = 90
c = 159.541	γ = 120

Symmetry
Space Group	P 63

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 EIGER2 XE 16M		2020-09-23	M	SINGLE WAVELENGTH
2	1	x-ray	45	PIXEL	DECTRIS PILATUS 12M		2020-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03
2	SYNCHROTRON	DIAMOND BEAMLINE I23	2.7552	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.39	51.57	100	0.135	0.031	0.999	13.3	19.3		110449

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.39	1.41	99.7		2.756	0.826	0.35	0.4	11.8

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.39	51.568	110151	5537	99.966	0.238	0.2372	0.2588	18.765

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]
-0.099	-0.05		-0.099		0.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.099
r_dihedral_angle_4_deg	14.574
r_dihedral_angle_3_deg	13.656
r_dihedral_angle_1_deg	7.155
r_lrange_it	4.845
r_lrange_other	4.623
r_scangle_it	2.395
r_scangle_other	2.344
r_mcangle_it	1.875
r_mcangle_other	1.875
r_angle_refined_deg	1.826
r_scbond_it	1.593
r_scbond_other	1.523
r_angle_other_deg	1.496
r_mcbond_it	1.222
r_mcbond_other	1.221
r_nbd_other	0.238
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.205
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_other	0.114
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_1	0.072
r_xyhbond_nbd_other	0.037
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3797
Nucleic Acid Atoms
Solvent Atoms	413
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing