Experiment: 4WOQ

Crystal Structures of CdNal from Clostridium difficile in complex with ketobutyric

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F74

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	298	NaAc, PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.875	α = 90
b = 122.612	β = 95.72
c = 122.186	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2014-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1	NSRRC	BL13B1

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	2.2	25	99.8	0.098	0.111	0.051	7.4	4.6		120931

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	2.2	2.28	98.4		0.496	0.576	0.287	0.844		3.7	11863

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1f74	2.2	25	114743	5782	94.4	0.1838	0.1843	0.2433	0.2433	Random selection	37.0326

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]
-7.025		10.817	8.236		-1.211

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.165
c_scbond_it	2.145
c_mcangle_it	2.08
c_mcbond_it	1.331

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18568
Nucleic Acid Atoms
Solvent Atoms	1598
Heterogen Atoms	56

Software

Software
Software Name	Purpose
HKL-2000	data reduction
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction