5ICC

Crystal structure of (S)-norcoclaurine 6-O-methyltransferase with S-adenosyl-L-homocysteine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZG3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	Peg3350, Sodium Chloride, Phosphate Citrate buffer

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.64	α = 90
b = 108.99	β = 90
c = 40.91	γ = 90

Symmetry
Space Group	P 21 21 2

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	ADSC QUANTUM 315r		2009-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.9797	ESRF	BM30A

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	1.9		99.3	0.098	17.15			26573		-3	20.518

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	1.9	2	95.4		0.393	4.1

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	1zg3	1.9	43.81	26572	1329	100	0.1589	0.1565	0.2061	RANDOM	14.35

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]
1.4			-1.22		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.215
r_dihedral_angle_3_deg	12.795
r_dihedral_angle_4_deg	10.373
r_dihedral_angle_1_deg	5.576
r_scangle_it	4.95
r_scbond_it	3.426
r_mcangle_it	2.158
r_angle_refined_deg	1.522
r_mcbond_it	1.356
r_chiral_restr	0.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.215
r_dihedral_angle_3_deg	12.795
r_dihedral_angle_4_deg	10.373
r_dihedral_angle_1_deg	5.576
r_scangle_it	4.95
r_scbond_it	3.426
r_mcangle_it	2.158
r_angle_refined_deg	1.522
r_mcbond_it	1.356
r_chiral_restr	0.129
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2727
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	74

Software

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

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 R01GM133198.