4AWD

Crystal structure of the beta-porphyranase BpGH16B (BACPLE_01689) from the human gut bacterium Bacteroides plebeius

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		23-25 % PEG 3350, 100 MM TRIS PH 8.5 AND 5 MM CALCIUM CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.69	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.12	α = 90
b = 107.23	β = 90
c = 137.26	γ = 90

Symmetry
Space Group	P 2 21 21

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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

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	2.4	43.74	99.9	0.13	10.5	6.3		30374		2

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	2.4	2.5	99.7		0.44	4.2	6.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3JUU	2.4	40	28740	1534	99.72	0.20261	0.20003	0.25014	RANDOM	19.518

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]
-6.41			25.27		-18.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.23
r_dihedral_angle_4_deg	21.125
r_dihedral_angle_3_deg	17.068
r_dihedral_angle_1_deg	6.955
r_scangle_it	2.523
r_scbond_it	1.527
r_angle_refined_deg	1.294
r_mcangle_it	1.091
r_mcbond_it	0.57
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4788
Nucleic Acid Atoms
Solvent Atoms	374
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing