7NIT

X-ray structure of a multidomain BbgIII from Bifidobacterium bifidum

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	1.6 M ammonium sulfate, sodium acetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.4	65.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.947	α = 86.991
b = 130.042	β = 84.83
c = 200.58	γ = 83.788

Symmetry
Space Group	P 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	PIXEL	DECTRIS EIGER2 XE 16M		2019-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.89	199.58	96.2	0.087	0.123	0.087	0.997	4.9	3.6		252478			84.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.89	2.94	98.4		1.514	2.141	1.514	0.355	0.5	3.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5dmy, 1gof, 2w1s, 2wdc, 3f2z and 4lpl	2.89	199.578	252014	12540	96.234	0.216	0.2141	0.247	113.059

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]
-4.589	-1.162	1.388	1.185	-5.199	2.947

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.641
r_lrange_it	23.574
r_dihedral_angle_4_deg	18.941
r_scangle_it	17.854
r_mcangle_it	16.808
r_dihedral_angle_3_deg	16.354
r_scbond_it	12.603
r_mcbond_it	11.412
r_dihedral_angle_1_deg	6.912
r_angle_refined_deg	1.259
r_nbtor_refined	0.302
r_symmetry_nbd_refined	0.274
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.122
r_symmetry_xyhbond_nbd_refined	0.099
r_chiral_restr	0.086
r_ncsr_local_group_11	0.069
r_ncsr_local_group_13	0.067
r_ncsr_local_group_4	0.066
r_ncsr_local_group_1	0.063
r_ncsr_local_group_6	0.062
r_ncsr_local_group_7	0.062
r_ncsr_local_group_9	0.062
r_ncsr_local_group_15	0.06
r_ncsr_local_group_12	0.056
r_ncsr_local_group_8	0.054
r_ncsr_local_group_10	0.054
r_ncsr_local_group_14	0.052
r_ncsr_local_group_2	0.049
r_ncsr_local_group_3	0.049
r_ncsr_local_group_5	0.046
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	55787
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	74

Software

Software
Software Name	Purpose
autoPROC	data scaling
Aimless	data reduction
MOLREP	phasing
REFMAC	refinement