9OU5 | pdb_00009ou5

Crystal Structure of Salmonella FraB Deglycase, Crystal Form 3

X-RAY DIFFRACTION

---

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, 0.1 M MES, pH 6.0-6.5

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.574	α = 90
b = 110.614	β = 90
c = 115.53	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		2021-03-24	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	1.669	79.9	76.4	0.076	0.022	16.7	12.9		67143

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	1.67	1.828			1.419	0.442	1.6

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	1.669	79.897	67143	3329	76.39	0.172	0.1708	0.1811	0.2021	0.2119	31.89

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]
0.126			-0.099		-0.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.508
r_dihedral_angle_3_deg	13.821
r_dihedral_angle_2_deg	8.232
r_lrange_it	7.827
r_lrange_other	7.744
r_dihedral_angle_1_deg	6.527
r_scangle_it	6.448
r_scangle_other	6.447
r_scbond_it	4.256
r_scbond_other	4.252
r_mcangle_it	3.885
r_mcangle_other	3.884
r_mcbond_it	2.947
r_mcbond_other	2.945
r_angle_refined_deg	1.712
r_angle_other_deg	0.6
r_nbd_refined	0.22
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.169
r_nbd_other	0.156
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_other	0.128
r_symmetry_nbd_refined	0.1
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.008
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	4831
Nucleic Acid Atoms
Solvent Atoms	414
Heterogen Atoms

Software

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