5T6B

X-ray structure of the KijD1 C3-methyltransfeerase, converted to monomeric form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5T64

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	18-22% PEG-3350, 2%MPD, 100 mM MES, 10 mM TDP, 5 mM SAH

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.707	α = 96.05
b = 82.455	β = 110.7
c = 82.825	γ = 112.09

Symmetry
Space Group	P 1

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	Bruker Platinum 135		2015-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2	75	96.6	0.074	7.3	3.1		90291

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	2	2.1	91		0.305	2.1	1.8

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	5T64	2	30	85763	4528	96.6	0.17855	0.17556	0.23424	RANDOM	25.19

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]
-0.72	-0.11	0.09	0.45	0.6	-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.969
r_dihedral_angle_4_deg	18.325
r_dihedral_angle_3_deg	15.553
r_dihedral_angle_1_deg	6.659
r_long_range_B_refined	5.44
r_long_range_B_other	5.439
r_scangle_other	3.817
r_mcangle_it	2.961
r_mcangle_other	2.961
r_scbond_it	2.389
r_scbond_other	2.368
r_mcbond_it	1.879
r_mcbond_other	1.879
r_angle_refined_deg	1.773
r_angle_other_deg	1.038
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12428
Nucleic Acid Atoms
Solvent Atoms	737
Heterogen Atoms	216

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing