8CBB | pdb_00008cbb

Structure of homodimeric luciferase from Enhygromyxa salina

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG3350 25%, lithium sulfate 0.2 M, BIS-TRIS 0.1 M pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.821	α = 88.72
b = 73.374	β = 77.93
c = 93.972	γ = 87.1

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 S 16M		2021-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9762	ESRF	ID23-1

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	2.71	91.89	97	0.068	0.096	0.068	0.981	4	1.8		35543

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	2.71	2.84		96.2	0.218	0.308	0.218	0.894		1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.71	91.89	33799	1743	97.06	0.19478	0.19096	0.2	0.26877	0.27	RANDOM	38.378

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]
0.67	1.4	2.21	-0.77	-0.66	1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.994
r_dihedral_angle_2_deg	16.545
r_dihedral_angle_1_deg	8.731
r_long_range_B_refined	6.401
r_long_range_B_other	6.394
r_scangle_other	4.336
r_mcangle_it	3.847
r_mcangle_other	3.846
r_scbond_it	2.629
r_scbond_other	2.609
r_mcbond_it	2.346
r_mcbond_other	2.344
r_angle_refined_deg	0.338
r_angle_other_deg	0.144
r_chiral_restr	0.02
r_bond_other_d	0.002
r_bond_refined_d	0.001
r_gen_planes_refined	0.001
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10876
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	20

Software

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