6XBV

Streptomyces coelicolor methylmalonyl-CoA epimerase (S115T) in complex with 2-nitronate-propionyl-CoA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JC5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	100 mM Bis-Tris:HCl pH 7.0, 700 mM ammonium sulfate, and 5% PEG400

Crystal Properties
Matthews coefficient	Solvent content
3.79	67.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.309	α = 90
b = 69.309	β = 90
c = 103.562	γ = 90

Symmetry
Space Group	P 41 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	80	IMAGE PLATE	MAR scanner 300 mm plate	MD2 microdifractometer	2019-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim 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	1.5	30	99.9	0.112	0.101	0.116	0.031	0.994	492.4	13.9		41252			27.733

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	99.9		1.092	0.967	1.134	0.301	0.84	7	13.8

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	1JC5	1.5	26.61	39173	2012	99.78	0.1544	0.1531	0.1791	RANDOM	27.733

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]
0.03			0.03		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.923
r_dihedral_angle_4_deg	12.977
r_dihedral_angle_3_deg	12.855
r_dihedral_angle_1_deg	7.495
r_angle_refined_deg	2.375
r_angle_other_deg	1.911
r_chiral_restr	0.273
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.923
r_dihedral_angle_4_deg	12.977
r_dihedral_angle_3_deg	12.855
r_dihedral_angle_1_deg	7.495
r_angle_refined_deg	2.375
r_angle_other_deg	1.911
r_chiral_restr	0.273
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1110
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
ARP/wARP	model building
HKL-2000	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 R01GM157729.