9OTR | pdb_00009otr

Crystal Structure of Salmonella FraB Deglycase, Crystal Form 4 with deletion of C-terminal residues 313-325.

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		298	20% w/v PEG3350, 0.2 M sodium sulfate, 0.1 M Bis-Tris propane, pH 8.0-8.5

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.482	α = 90
b = 108.363	β = 90
c = 119.151	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.979330	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	1.839	49.434	71.2	0.065	0.041	16.7	5.9		45084

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.839	1.987			0.919	0.419	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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.839	49.434	45084	2238	71.223	0.174	0.1724	0.1821	0.2042	0.2105	35.602

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]
-0.141			-0.184		0.325

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.44
r_dihedral_angle_6_deg	13.905
r_lrange_it	8.473
r_lrange_other	8.449
r_dihedral_angle_2_deg	7.548
r_dihedral_angle_1_deg	7.197
r_scangle_it	6.587
r_scangle_other	6.586
r_mcangle_it	4.424
r_mcangle_other	4.424
r_scbond_it	4.296
r_scbond_other	4.295
r_mcbond_it	3.129
r_mcbond_other	3.126
r_angle_refined_deg	1.684
r_angle_other_deg	0.574
r_nbd_refined	0.217
r_nbd_other	0.201
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.175
r_symmetry_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.161
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.084
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4697
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms

Software

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