4XXT

Crystal structure of Fused Zn-dependent amidase/peptidase/peptodoglycan-binding domain-containing protein from Clostridium acetobutylicum ATCC 824

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.2M Calcium Acetate, 0.1M Tris-HCl, 20% PEG3000

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.79	α = 90
b = 60.79	β = 90
c = 125.551	γ = 120

Symmetry
Space Group	P 31 2 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 210r		2013-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97925	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	1.77	50	99.6	0.042	0.044	0.015	13.5	8.1		26936		-3

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	1.77	1.8	93.4		0.505	0.552	0.218	0.911	2.84	6	1226

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.77	27.36	25217	1334	98.66	0.169	0.1676	0.1959	RANDOM	26.48

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]
0.13	0.07		0.13		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.089
r_dihedral_angle_4_deg	13.816
r_dihedral_angle_3_deg	10.627
r_dihedral_angle_1_deg	5.378
r_mcangle_it	1.279
r_angle_refined_deg	1.106
r_angle_other_deg	0.716
r_mcbond_it	0.699
r_mcbond_other	0.694
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.089
r_dihedral_angle_4_deg	13.816
r_dihedral_angle_3_deg	10.627
r_dihedral_angle_1_deg	5.378
r_mcangle_it	1.279
r_angle_refined_deg	1.106
r_angle_other_deg	0.716
r_mcbond_it	0.699
r_mcbond_other	0.694
r_chiral_restr	0.071
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1707
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	26

Software

Software
Software Name	Purpose
HKL-3000	data reduction
SBC-Collect	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.