9OTJ | pdb_00009otj

Crystal Structure of Salmonella FraB Deglycase, Crystal Form 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FKJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	15% v/v 2-propanol, 0.1 M magnesium chloride, 0.1 M MES, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.292	α = 90
b = 108.515	β = 90
c = 120.856	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		2020-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97930	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	1.85	80.743	86	0.049	0.021	16.1	6.3		53947

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	1.851	1.975	24.7		1.57	0.648		6.9

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	1.851	80.743	53814	2620	85.724	0.198	0.1955	0.2047	0.2538	0.2634	50.417

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]
0.032			-0.224		0.191

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.88
r_dihedral_angle_6_deg	14.412
r_dihedral_angle_2_deg	14.375
r_lrange_it	11.348
r_lrange_other	11.305
r_scangle_it	8.736
r_scangle_other	8.735
r_mcangle_it	7.486
r_mcangle_other	7.485
r_dihedral_angle_1_deg	7.135
r_scbond_it	6.163
r_scbond_other	6.161
r_mcbond_it	5.467
r_mcbond_other	5.464
r_angle_refined_deg	1.96
r_angle_other_deg	0.66
r_symmetry_nbd_refined	0.268
r_nbd_other	0.231
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.2
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.191
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_other	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4801
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms

Software

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