3SD7

1.7 Angstrom Resolution Crystal Structure of Putative Phosphatase from Clostridium difficile

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	Protein: 7.1mG/mL, 0.5M Sodium chloride, 0.01M Tris, pH 8.3, Screen: JCSG+, D12, 0.04M Potassium Phosphate, 16% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.333	α = 90
b = 116.333	β = 90
c = 36.08	γ = 90

Symmetry
Space Group	I 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MARMOSAIC 225 mm CCD	Beryllium lenses	2011-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.7	30	99.2	0.048	35	7.2	26648	26648		-3	29.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	91.1		0.541	2.8	5.3	1216

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3MC1	1.7	29.65	25299	25299	1344	99.11	0.16877	0.16877	0.16745	0.19298	RANDOM	39.35

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]
-0.78			-0.78		1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.621
r_dihedral_angle_3_deg	10.392
r_dihedral_angle_4_deg	5.366
r_scangle_it	4.994
r_scbond_it	3.083
r_dihedral_angle_1_deg	3.044
r_mcangle_it	2.049
r_angle_refined_deg	1.298
r_mcbond_it	1.226
r_angle_other_deg	0.827

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.621
r_dihedral_angle_3_deg	10.392
r_dihedral_angle_4_deg	5.366
r_scangle_it	4.994
r_scbond_it	3.083
r_dihedral_angle_1_deg	3.044
r_mcangle_it	2.049
r_angle_refined_deg	1.298
r_mcbond_it	1.226
r_angle_other_deg	0.827
r_mcbond_other	0.381
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1759
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	24

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.