2RF8 | pdb_00002rf8

Crystal Structure of the mutant C2A conjugated bile acid hydrolase from Clostridium perfringens

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BJG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	10 mM BisTris pH 5.5, 20 mM ammonium sulfate, 25% PEG 3350, vapor diffusion, sitting drop, temperature 291K, Vapor diffusion, sitting drop

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.64	α = 90
b = 64.64	β = 90
c = 338.833	γ = 90

Symmetry
Space Group	P 41 2 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	MAR CCD 165 mm	toroidal mirrors	2005-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	2.8	30	90.7	0.142	12.6	8.3		17112			41

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	90.3		0.462	3.3	8.5	1631

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	2bjg	2.9	30	15424	763	90.78	0.209	0.206	0.2	0.275	0.26	RANDOM	24.891

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]
1.31			1.31		-2.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.712
r_dihedral_angle_3_deg	14.353
r_dihedral_angle_4_deg	8.597
r_dihedral_angle_1_deg	4.979
r_angle_refined_deg	0.886
r_scangle_it	0.394
r_mcangle_it	0.375
r_nbtor_refined	0.296
r_scbond_it	0.241
r_mcbond_it	0.216

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.712
r_dihedral_angle_3_deg	14.353
r_dihedral_angle_4_deg	8.597
r_dihedral_angle_1_deg	4.979
r_angle_refined_deg	0.886
r_scangle_it	0.394
r_mcangle_it	0.375
r_nbtor_refined	0.296
r_scbond_it	0.241
r_mcbond_it	0.216
r_nbd_refined	0.164
r_symmetry_vdw_refined	0.121
r_xyhbond_nbd_refined	0.106
r_symmetry_hbond_refined	0.084
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5222
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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.