9U3B | pdb_00009u3b

Monomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed with L-Thioproline

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EL5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	1.5 M Ammonium sulfate, 100 mM Tris-HCl buffer pH8.5

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.876	α = 90
b = 69.401	β = 93.722
c = 73.028	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2022-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.3	42.24	93.2	0.062	0.993	6.8	2.1		165675

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32			0.505	0.651	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	1EL5	1.3	40.505	165671	8108	92.977	0.154	0.1529	0.1629	0.1753	0.1835	14.385

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]
-0.006			0.001		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.452
r_dihedral_angle_3_deg	11.511
r_dihedral_angle_1_deg	7.189
r_dihedral_angle_other_2_deg	6.912
r_dihedral_angle_2_deg	5.827
r_lrange_it	4.709
r_lrange_other	4.709
r_scangle_it	3.838
r_scangle_other	3.838
r_scbond_it	2.527
r_scbond_other	2.526
r_mcangle_it	1.996
r_mcangle_other	1.996
r_angle_refined_deg	1.921
r_mcbond_it	1.344
r_mcbond_other	1.344
r_angle_other_deg	0.65
r_symmetry_nbd_refined	0.297
r_nbd_other	0.257
r_nbd_refined	0.227
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.152
r_chiral_restr	0.097
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.081
r_chiral_restr_other	0.064
r_gen_planes_refined	0.013
r_bond_refined_d	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5991
Nucleic Acid Atoms
Solvent Atoms	622
Heterogen Atoms	169

Software

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