6I73 | pdb_00006i73

Structure of Fragaria ananassa O-methyltransferase in complex with S-adenosylhomocysteine and protocatechuic aldehyde

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.4-0.6 M Ammonium sulfate, 1 M Lithium sulfate, 0.1 M Sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.376	α = 90
b = 87.655	β = 90
c = 146.814	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARMOSAIC 225 mm CCD		2017-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.3	0.8943	BESSY	14.3

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	1.35	29.31	100	0.09	0.096	0.999	15.37	8.82		187792			18.926

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	1.35	1.45	99.9		0.882	0.95	0.691	2.15	7.373

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1KYW	1.35	29.31	184027	3764	99.96	0.1222	0.1217	0.1213	0.148	0.1469	RANDOM	15.123

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]
0.18			-0.56		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.276
r_dihedral_angle_4_deg	22.998
r_sphericity_free	19.522
r_dihedral_angle_3_deg	11.698
r_sphericity_bonded	7.391
r_dihedral_angle_1_deg	6.277
r_rigid_bond_restr	2.244
r_angle_refined_deg	1.678
r_angle_other_deg	1.136
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.276
r_dihedral_angle_4_deg	22.998
r_sphericity_free	19.522
r_dihedral_angle_3_deg	11.698
r_sphericity_bonded	7.391
r_dihedral_angle_1_deg	6.277
r_rigid_bond_restr	2.244
r_angle_refined_deg	1.678
r_angle_other_deg	1.136
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5398
Nucleic Acid Atoms
Solvent Atoms	1014
Heterogen Atoms	103

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
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.