6Q11

Crystal structure of MurA from Clostridium difficile, mutation C116S, in the presence of URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID

X-RAY DIFFRACTION

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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, 1M NMe4Cl, 100 mM MOPS. Crystals were then soaked in 10% PEG 8000, 1M NMe4Cl, 5 mM PEP, 200 mM NaCl, 100 mM MOPS before data collection

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.951	α = 90
b = 137.951	β = 90
c = 137.951	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	0.9981	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.7	50	99.5	0.079	0.081	0.018	28.9	13.8		47699

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	99.2		0.44	0.485	0.198	0.009	2.9	5.6

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	1.8	34.51	38120	2128	99.51	0.19034	0.1884	0.22587	RANDOM	31.241

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	32.57
r_dihedral_angle_4_deg	20.477
r_dihedral_angle_3_deg	15.558
r_long_range_B_refined	6.814
r_long_range_B_other	6.813
r_dihedral_angle_1_deg	6.147
r_scangle_other	6.034
r_scbond_it	3.942
r_scbond_other	3.941
r_mcangle_it	3.344
r_mcangle_other	3.344
r_mcbond_it	2.404
r_mcbond_other	2.404
r_angle_refined_deg	1.521
r_angle_other_deg	0.496
r_chiral_restr	0.067
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	3106
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing