7PI1 | pdb_00007pi1

Bacillus subtilis PabB

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	0.06 M magnesium chloride hexahydrate, 0.06 M calcium chloride dihydrate, 20 % v/v PEG 500 MME, 10 % w/v PEG 20000, 0.01 M tris (base); BICINE, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.084	α = 90
b = 170.698	β = 90
c = 224.99	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS3 6M		2021-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.920	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.729	51.08	100	0.094	0.996	4.4	12.9		206370			22.91

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.729	1.76			0.256	0.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	Model used not yet deposited	1.729	50.826	206243	10342	99.891	0.201	0.1989	0.21	0.236	0.24	35.435

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]
0.044			0.01		-0.054

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.664
r_dihedral_angle_3_deg	17.073
r_dihedral_angle_4_deg	16.831
r_lrange_it	7.631
r_lrange_other	7.575
r_dihedral_angle_1_deg	7.356
r_scangle_it	5.505
r_scangle_other	5.505
r_mcangle_it	3.806
r_mcangle_other	3.806
r_scbond_it	3.39
r_scbond_other	3.39
r_mcbond_it	2.476
r_mcbond_other	2.474
r_angle_other_deg	2.328
r_angle_refined_deg	1.482
r_symmetry_xyhbond_nbd_refined	0.252
r_nbd_other	0.243
r_symmetry_nbd_other	0.21
r_symmetry_nbd_refined	0.208
r_nbd_refined	0.194
r_metal_ion_refined	0.179
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.165
r_symmetry_xyhbond_nbd_other	0.114
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.067
r_bond_other_d	0.035
r_gen_planes_other	0.009
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14629
Nucleic Acid Atoms
Solvent Atoms	1125
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing