7R4P

Structure of human hydroxyacid oxidase 1 bound with 6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1 M MIB, pH 7, 30% PEG1000

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.13	α = 90
b = 97.13	β = 90
c = 80.84	γ = 90

Symmetry
Space Group	I 4

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 PILATUS 6M		2019-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.37	68.68	98.1	0.033	0.036	0.014	1	20.3	5.5		77168

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.37	1.41	82.3		0.819	0.994	0.547	0.523		2.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6GMB	1.37	68.68	73234	3937	98.07	0.1808	0.1799	0.196	RANDOM	22.088

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]
-0.41			-0.41		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.266
r_dihedral_angle_4_deg	16.814
r_dihedral_angle_3_deg	12.238
r_dihedral_angle_1_deg	7.231
r_angle_refined_deg	2.488
r_angle_other_deg	1.721
r_chiral_restr	0.183
r_bond_refined_d	0.023
r_gen_planes_refined	0.015
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.266
r_dihedral_angle_4_deg	16.814
r_dihedral_angle_3_deg	12.238
r_dihedral_angle_1_deg	7.231
r_angle_refined_deg	2.488
r_angle_other_deg	1.721
r_chiral_restr	0.183
r_bond_refined_d	0.023
r_gen_planes_refined	0.015
r_bond_other_d	0.005
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2538
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.