5MXB

Crystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	292	1.4 M sodium citrate pH 6.3

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.469	α = 90
b = 74.469	β = 90
c = 67.11	γ = 120

Symmetry
Space Group	P 65

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	MARMOSAIC 225 mm CCD		2012-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918410	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.51	37.23	99.7	0.04	0.047	18.48	4.069		33163		-3	30.38

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.51	1.6	99.4		0.695	0.803	2.18	3.998

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2qim	1.51	37.23	32068	1095	99.71	0.1838	0.1829	0.2107	RANDOM	29.189

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]
-0.81	-0.81		-0.81		2.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.85
r_dihedral_angle_3_deg	14
r_dihedral_angle_1_deg	5.793
r_dihedral_angle_4_deg	5.784
r_angle_refined_deg	1.933
r_angle_other_deg	0.793
r_chiral_restr	0.115
r_bond_refined_d	0.019
r_gen_planes_refined	0.015
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.85
r_dihedral_angle_3_deg	14
r_dihedral_angle_1_deg	5.793
r_dihedral_angle_4_deg	5.784
r_angle_refined_deg	1.933
r_angle_other_deg	0.793
r_chiral_restr	0.115
r_bond_refined_d	0.019
r_gen_planes_refined	0.015
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1163
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.