3IF9

Crystal structure of Glycine Oxidase G51S/A54R/H244A mutant in complex with inhibitor glycolate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	100mM Hepes/Na, pH 7.5, 28 % w/v PEG 400, 200mM CaCl2, 30mM glycolate/Na, 3 % glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.344	α = 90
b = 215.058	β = 90
c = 217.083	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	RAYONIX MX-225		2009-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	1.04063	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	76.25		0.086		10.1		52481		3	43.993

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74	100		0.344	10.7	10.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1RYI	2.6	76.25	49195	2639	98.76	0.19866	0.19561	0.25654	RANDOM	30.946

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]
-1.18			1.02		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.009
r_dihedral_angle_3_deg	16.923
r_dihedral_angle_4_deg	16.138
r_dihedral_angle_1_deg	6.027
r_scangle_it	1.966
r_angle_refined_deg	1.309
r_scbond_it	1.199
r_mcangle_it	1.094
r_mcbond_it	0.611
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.009
r_dihedral_angle_3_deg	16.923
r_dihedral_angle_4_deg	16.138
r_dihedral_angle_1_deg	6.027
r_scangle_it	1.966
r_angle_refined_deg	1.309
r_scbond_it	1.199
r_mcangle_it	1.094
r_mcbond_it	0.611
r_nbtor_refined	0.309
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.209
r_symmetry_vdw_refined	0.202
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11332
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	232

Software

Software
Software Name	Purpose
MxCuBE	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.