2HEZ | pdb_00002hez

Bifidobacterium longum bile salt hydrolase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PVA	PDB ENTRY 3PVA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	303	ammonium sulfate 30% w/v, 0.5 M sodium formate, sucrose (1M) 100ml, 40 uL of b-octyl glucosidase (0.50% w/v), pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.243	α = 90
b = 125.243	β = 90
c = 117.028	γ = 120

Symmetry
Space Group	P 32 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	IMAGE PLATE	RIGAKU RAXIS IV	Mirrors	2003-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.49	20		0.06				37135	3	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.55	100

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	PDB ENTRY 3PVA	2.5	20	35045	1844	99.65	0.17659	0.17443	0.17	0.216	0.21	RANDOM	43.015

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]
-0.38	-0.19		-0.38		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.85
r_dihedral_angle_4_deg	22.874
r_dihedral_angle_3_deg	18.621
r_dihedral_angle_1_deg	7.242
r_scangle_it	4.702
r_scbond_it	3.138
r_angle_refined_deg	2.184
r_mcangle_it	2.065
r_mcbond_it	1.236
r_nbtor_refined	0.324
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.233
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.154
r_chiral_restr	0.144
r_bond_refined_d	0.024
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4932
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
AMoRE	phasing