8PNE

E.coli YihX Wild Type Apo

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B0C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	20-60 mg/mL YihX protein in the buffer of Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM, was mixed 1:1 ratio with the precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 30 mM MgCl2, 30 mM CaCl2, 20% glycerol, 10% PEG4000, 20% PEG500

Crystal Properties
Matthews coefficient	Solvent content
4.16	70.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.216	α = 90
b = 79.567	β = 90
c = 148.188	γ = 90

Symmetry
Space Group	I 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 EIGER2 XE 16M		2022-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	70.2	100	0.998	12.9	13.6		31737

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	1.9	1.94			0.837

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	70.2	31733	1549	99.987	0.205	0.2037	0.2339	42.98

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]
-2.854			-4.725		7.578

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.829
r_dihedral_angle_3_deg	14.2
r_lrange_it	9.32
r_lrange_other	9.207
r_dihedral_angle_2_deg	8.88
r_scangle_it	7.346
r_scangle_other	7.343
r_dihedral_angle_1_deg	6.904
r_mcangle_other	5.597
r_mcangle_it	5.582
r_scbond_it	5.368
r_scbond_other	5.364
r_mcbond_other	4.108
r_mcbond_it	4.103
r_angle_refined_deg	1.491
r_angle_other_deg	0.521
r_symmetry_nbd_refined	0.425
r_nbd_other	0.307
r_nbd_refined	0.228
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.138
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1604
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	31

Software

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