6Q0Y | pdb_00006q0y

Crystal structure of MurA from Clostridium difficile, mutant C116S, in the presence of Uridine-Diphosphate-N-Acetylglucosamine

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	298	10% PEG 8000, 1M NMe4Cl, 100 mM MOPS

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.647	α = 90
b = 138.647	β = 90
c = 138.647	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	99.9	0.078	0.08	0.016	12.6	18.3		48924

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	100		0.437	0.461	0.145	0.377	3.7	9.4

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	6q03	1.7	34.69	46582	2342	99.87	0.1743	0.1725	0.18	0.2092	0.21	RANDOM	26.862

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	38.665
r_dihedral_angle_4_deg	16.562
r_dihedral_angle_3_deg	15.716
r_dihedral_angle_1_deg	6.244
r_angle_refined_deg	1.672
r_angle_other_deg	1.602
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.665
r_dihedral_angle_4_deg	16.562
r_dihedral_angle_3_deg	15.716
r_dihedral_angle_1_deg	6.244
r_angle_refined_deg	1.672
r_angle_other_deg	1.602
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3106
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	43

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.