8IOX | pdb_00008iox

Escherichia coli OpgD mutant-D388N

X-RAY DIFFRACTION

---

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	PEG2000MME, TMAO, tris-HCl (pH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
4.71	73.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 226.75	α = 90
b = 392.76	β = 90
c = 324.648	γ = 90

Symmetry
Space Group	C 2 2 2

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 S 6M		2022-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.95	49.143	100	0.208	0.994	13	13.7		301232

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	2.95	3			0.869

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.95	49.143	301231	14722	99.939	0.196	0.1937	0.2	0.2322	0.23	34.688

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]
-1.584			-0.932		2.516

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.722
r_dihedral_angle_4_deg	20.014
r_dihedral_angle_3_deg	18.449
r_dihedral_angle_1_deg	7.239
r_lrange_other	7.182
r_lrange_it	7.181
r_scangle_it	5.028
r_scangle_other	5.028
r_mcangle_other	4.337
r_mcangle_it	4.336
r_scbond_it	3.149
r_scbond_other	3.149
r_mcbond_it	2.733
r_mcbond_other	2.733
r_angle_other_deg	2.332
r_angle_refined_deg	1.602
r_symmetry_nbd_refined	0.266
r_nbd_other	0.248
r_symmetry_nbd_other	0.232
r_nbd_refined	0.21
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.178
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_other	0.11
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.065
r_bond_other_d	0.035
r_bond_refined_d	0.009
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	50952
Nucleic Acid Atoms
Solvent Atoms	666
Heterogen Atoms	230

Software

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