9OU6 | pdb_00009ou6

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	9OTJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	10-14% v/v PEG300, 0.1bM MES, pH 6.0-6.5

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.708	α = 90
b = 109.334	β = 90
c = 114.53	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		2023-04-06	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	1.483	79.084	77.3	0.068	0.029	11.2	6.7		93089

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	1.483	1.601			0.816	0.368

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	1.483	79.084	93089	4610	77.255	0.17	0.1686	0.1684	0.2014	0.2014	21.571

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]
-0.021			-0.025		0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.367
r_dihedral_angle_3_deg	12.905
r_dihedral_angle_2_deg	7.464
r_lrange_it	7.236
r_lrange_other	7.155
r_dihedral_angle_1_deg	6.305
r_scangle_it	5.811
r_scangle_other	5.811
r_scbond_it	3.778
r_scbond_other	3.778
r_mcangle_it	3.264
r_mcangle_other	3.264
r_mcbond_it	2.276
r_mcbond_other	2.276
r_angle_refined_deg	1.82
r_angle_other_deg	0.605
r_symmetry_xyhbond_nbd_other	0.265
r_nbd_refined	0.23
r_symmetry_nbd_refined	0.22
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.171
r_nbd_other	0.154
r_symmetry_xyhbond_nbd_refined	0.116
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.079
r_gen_planes_refined	0.01
r_bond_refined_d	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	4818
Nucleic Acid Atoms
Solvent Atoms	476
Heterogen Atoms

Software

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