8BNW

X-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8BF6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	17% PEG 3350; 0.1M MES, pH 6.5, 0.1M MgAc; Cryo- EthGl

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.369	α = 90
b = 118.433	β = 90
c = 141.046	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER2 X 16M		2021-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976300	Diamond	I03

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	2.13	70.623	100	0.069	0.074	0.028	1	17.8	12.7		17078

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	2.13	2.19			3.272	3.543	1.352	0.377		12.9

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	8BF6	2.133	70.623	17045	862	99.93	0.224	0.2216	0.2661	76.498

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]
1.572			0.088		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.985
r_dihedral_angle_6_deg	14.585
r_lrange_it	10.572
r_lrange_other	10.572
r_scangle_it	8.103
r_dihedral_angle_1_deg	8.1
r_scangle_other	7.825
r_mcangle_it	6.954
r_mcangle_other	6.952
r_scbond_it	5.681
r_scbond_other	5.414
r_mcbond_it	4.962
r_mcbond_other	4.96
r_dihedral_angle_2_deg	2.305
r_angle_refined_deg	1.246
r_symmetry_nbd_refined	0.447
r_angle_other_deg	0.388
r_symmetry_metal_ion_refined	0.324
r_symmetry_xyhbond_nbd_refined	0.29
r_nbd_refined	0.234
r_nbd_other	0.224
r_xyhbond_nbd_refined	0.207
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.179
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.07
r_chiral_restr	0.052
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2167
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	15

Software

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