4N3V | pdb_00004n3v

Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.89 A resolution with product added

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4L8P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	10.00% polyethylene glycol 6000, 0.1M citric acid pH 5.0, Additive: 0.001 M 3-oxo-delta 4,6, Lithocholyl Coenzyme A, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.282	α = 90
b = 84.282	β = 90
c = 311.823	γ = 120

Symmetry
Space Group	H 3 2

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	KOHZU: Double Crystal Si(111)	2012-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2		ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.89	47.414	99.9	0.069	0.073	19.5			34715		-3	26.185

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.94	98.8		0.885	0.953	0.35	2.5	7.2

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	4L8P	1.89	47.414	34711	1748	99.87	0.1894	0.1879	0.2	0.2183	0.22	RANDOM	35.823

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]
0.55	0.55		0.55		-1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.127
r_dihedral_angle_3_deg	12.194
r_dihedral_angle_4_deg	10.436
r_dihedral_angle_1_deg	6.348
r_mcangle_it	4.372
r_mcbond_it	3.334
r_mcbond_other	3.318
r_angle_refined_deg	1.375
r_angle_other_deg	0.823
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.127
r_dihedral_angle_3_deg	12.194
r_dihedral_angle_4_deg	10.436
r_dihedral_angle_1_deg	6.348
r_mcangle_it	4.372
r_mcbond_it	3.334
r_mcbond_other	3.318
r_angle_refined_deg	1.375
r_angle_other_deg	0.823
r_chiral_restr	0.097
r_bond_refined_d	0.01
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	2722
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	124

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
PHASER	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction

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.