9U3E | pdb_00009u3e

Monomeric sarcosine oxidase from Bacillus sp. (SoxB) Y254A mutant

X-RAY DIFFRACTION

---

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	1.6 M Ammonium sulfate, 100 mM Tris-HCl buffer pH8.5

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.776	α = 90
b = 69.7	β = 93.749
c = 73.665	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		2022-06-23	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	1.35	42.41	93.7	0.082	0.996	8.8	4.3		150204

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	1.35	1.37			0.703	0.619	2.1

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	1.35	42.408	150178	7346	93.263	0.156	0.1554	0.1643	0.1776	0.1862	12.088

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]
0.003		-0.001	-0.001		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.389
r_dihedral_angle_3_deg	11.943
r_dihedral_angle_1_deg	7.26
r_dihedral_angle_2_deg	6.999
r_dihedral_angle_other_2_deg	5.138
r_lrange_it	3.88
r_lrange_other	3.779
r_scangle_it	3.191
r_scangle_other	3.191
r_scbond_it	2.148
r_scbond_other	2.148
r_angle_refined_deg	1.998
r_mcangle_it	1.728
r_mcangle_other	1.728
r_mcbond_it	1.186
r_mcbond_other	1.185
r_angle_other_deg	0.682
r_nbd_refined	0.228
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.183
r_nbd_other	0.179
r_symmetry_xyhbond_nbd_other	0.154
r_symmetry_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.138
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.083
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	5925
Nucleic Acid Atoms
Solvent Atoms	683
Heterogen Atoms	133

Software

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