7NIT | pdb_00007nit

X-ray structure of a multidomain BbgIII from Bifidobacterium bifidum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DMY	5dmy, 1gof, 2w1s, 2wdc, 3f2z and 4lpl
experimental model	PDB	1GOF	5dmy, 1gof, 2w1s, 2wdc, 3f2z and 4lpl
experimental model	PDB	2W1S	5dmy, 1gof, 2w1s, 2wdc, 3f2z and 4lpl
experimental model	PDB	2WDC	5dmy, 1gof, 2w1s, 2wdc, 3f2z and 4lpl
experimental model	PDB	3F2Z	5dmy, 1gof, 2w1s, 2wdc, 3f2z and 4lpl
experimental model	PDB	4LPL	5dmy, 1gof, 2w1s, 2wdc, 3f2z and 4lpl

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.21	0.247	0.25	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