6Q0A

Crystal structure of MurA from Clostridium difficile, mutation C116D, n the presence of UDP-N-acetylmuramic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q03

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	10% PEG 8000, 1 M NMe4Cl, 200 mM NaCl, 100 mM MOPS

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.409	α = 90
b = 139.409	β = 90
c = 139.409	γ = 90

Symmetry
Space Group	I 2 3

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 210r		2018-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9987	APS	19-BM

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	1.65	50	99.1	0.055	80.3	20.9		53427

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	89.1		0.39	4.8	11.1

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	6q03	1.65	29.74	50734	2693	99.61	0.1707	0.169	0.1998	RANDOM	27.509

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.807
r_dihedral_angle_4_deg	17.258
r_dihedral_angle_3_deg	14.489
r_dihedral_angle_1_deg	6.324
r_angle_refined_deg	1.732
r_angle_other_deg	1.618
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.807
r_dihedral_angle_4_deg	17.258
r_dihedral_angle_3_deg	14.489
r_dihedral_angle_1_deg	6.324
r_angle_refined_deg	1.732
r_angle_other_deg	1.618
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3111
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
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.