4L8P | pdb_00004l8p

Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.60 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	50.00% polyethylene glycol 200, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.905	α = 90
b = 58.905	β = 90
c = 91.34	γ = 120

Symmetry
Space Group	P 63

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2010-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.6	29.452	100	0.095	11.1	7.3	23715	23715			17.737

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64	100		0.651	0.651	2.7	7	1743

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.6	29.452	23680	1222	99.93	0.1526	0.1512	0.17	0.1808	0.2	RANDOM	24.7923

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]
0.73	0.73		0.73		-2.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.408
r_dihedral_angle_3_deg	12.031
r_dihedral_angle_4_deg	11.896
r_dihedral_angle_1_deg	6.669
r_mcangle_it	3.206
r_mcbond_it	2.12
r_mcbond_other	2.117
r_angle_refined_deg	1.488
r_angle_other_deg	0.895
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.408
r_dihedral_angle_3_deg	12.031
r_dihedral_angle_4_deg	11.896
r_dihedral_angle_1_deg	6.669
r_mcangle_it	3.206
r_mcbond_it	2.12
r_mcbond_other	2.117
r_angle_refined_deg	1.488
r_angle_other_deg	0.895
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1366
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	28

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

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.