9OTU | pdb_00009otu

Crystal Structure of Salmonella FraB Deglycase, E214A Mutant, Crystal Form 5

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	18% w/v PEG6000, 0.2 M magnesium chloride, 0.1 M MES, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.417	α = 90
b = 114.417	β = 90
c = 154.469	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 PILATUS3 6M		2022-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.979310	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.873	99.088	36.7	0.078	0.026	15.8	9.6		35409

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.873	2.152			0.886	0.354	2.2

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	1.873	99.088	35409	1718	36.72	0.272	0.2683	0.2734	0.3333	0.3367	40.453

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]
-0.022	-0.011		-0.022		0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.273
r_dihedral_angle_6_deg	14.564
r_dihedral_angle_1_deg	9.084
r_lrange_it	8.368
r_lrange_other	8.368
r_mcangle_it	5.697
r_mcangle_other	5.696
r_scangle_it	5.525
r_scangle_other	5.525
r_dihedral_angle_2_deg	5.464
r_mcbond_it	3.654
r_mcbond_other	3.654
r_scbond_it	3.417
r_scbond_other	3.416
r_angle_refined_deg	1.761
r_angle_other_deg	0.596
r_symmetry_xyhbond_nbd_refined	0.243
r_nbd_refined	0.242
r_symmetry_nbd_other	0.213
r_symmetry_nbd_refined	0.211
r_xyhbond_nbd_refined	0.208
r_nbtor_refined	0.194
r_nbd_other	0.169
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.08
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4649
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms

Software

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