9GYZ | pdb_00009gyz

Crystal structure of domain-of-unknown-function DUF4867 from Bacillus megaterium (unmodelled additional ligand density at active site)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9GYY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Direct soaking of sulfofructose ligand into a crystal of SqvD, which was obtained from protein solution at 60 mg mL-1 in 50 mM Tris buffer, 300 mM NaCl buffer pH 7.5 used to set up a drop containing 0.15 uL protein: 0.15 uL mother liquor, the latter comprising 0.1 M HEPES sodium 7.5 30 % v/v polyethylene glycol 400.

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.509	α = 90
b = 82.509	β = 90
c = 136.194	γ = 120

Symmetry
Space Group	P 32 2 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 X 16M		2021-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9763	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	2.1	49.3	100	0.101	0.104	0.025	0.999	17.2	16.7		32018

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	2.1	2.16		100	1.323	1.36	0.313	0.905		18.6

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	2.1	45.44	30237	1588	99.51	0.21014	0.2078	0.2153	0.25529	0.2576	RANDOM	48.115

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]
0.97	0.48		0.97		-3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.442
r_long_range_B_other	10.225
r_long_range_B_refined	10.219
r_scangle_other	9.647
r_dihedral_angle_2_deg	9.058
r_dihedral_angle_1_deg	7.807
r_scbond_it	7.789
r_scbond_other	7.787
r_mcangle_it	7.032
r_mcangle_other	7.032
r_mcbond_it	6.416
r_mcbond_other	6.416
r_angle_refined_deg	2.324
r_angle_other_deg	0.803
r_chiral_restr	0.12
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	3482
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
MOLREP	phasing