8B7X | pdb_00008b7x

X-ray structure of the CeuE Homologue from Geobacillus stearothermophilus - apo form.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Index D3: 0.1M HEPES, pH 7.0, 30% Jeffamine ED 2001, pH 7.0. No cryo.

Crystal Properties
Matthews coefficient	Solvent content
	26.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.519	α = 81.566
b = 35.725	β = 83.242
c = 52.29	γ = 65.06

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 PILATUS3 6M		2018-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	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	1.42	32.225	94.9	0.033	0.046	0.033	0.998	5.8	2		37722

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	1.42	1.44			0.323	0.457	0.323	0.862		1.7

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	3zkw	1.42	32.225	37657	1940	94.67	0.169	0.1655	0.17	0.2281	0.24	28.729

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]
0.43	0.076	1.675	-0.664	-1.253	0.549

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.887
r_dihedral_angle_6_deg	15.737
r_dihedral_angle_2_deg	9.768
r_lrange_other	7.156
r_lrange_it	7.152
r_scangle_it	6.871
r_scangle_other	6.469
r_dihedral_angle_1_deg	6.4
r_scbond_it	6.227
r_rigid_bond_restr	6.212
r_scbond_other	5.813
r_mcangle_it	5.43
r_mcangle_other	5.428
r_mcbond_other	4.417
r_mcbond_it	4.415
r_angle_refined_deg	1.377
r_angle_other_deg	0.48
r_nbd_refined	0.221
r_symmetry_xyhbond_nbd_refined	0.221
r_symmetry_nbd_other	0.193
r_symmetry_nbd_refined	0.193
r_nbd_other	0.182
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.152
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2174
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	24

Software

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