5MXW

Crystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin and trans-zeatin.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QIM

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
3.24	62.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.4	α = 90
b = 74.4	β = 90
c = 67.31	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		2012-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.0000000	MAX II	I911-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.57	46.59	99.7	0.037	0.041	0.999	22.2	4.984		29524		-3	31.574

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.57	1.66	98.4		0.744	0.834	0.789	2.01	4.892

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	THROUGHOUT	2qim	1.57	46.59	28468	1057	99.68	0.1858	0.185	0.2059	RANDOM	32.201

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]
-0.91	-0.91		-0.91		2.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.583
r_dihedral_angle_3_deg	15.508
r_dihedral_angle_1_deg	7.039
r_angle_refined_deg	1.866
r_angle_other_deg	0.791
r_dihedral_angle_4_deg	0.424
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_gen_planes_refined	0.014
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.583
r_dihedral_angle_3_deg	15.508
r_dihedral_angle_1_deg	7.039
r_angle_refined_deg	1.866
r_angle_other_deg	0.791
r_dihedral_angle_4_deg	0.424
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1162
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	50

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 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.