5XAO | pdb_00005xao

Crystal structure of Phaeospaeria nodrum fructosyl peptide oxidase mutant Asn56Ala in complexes with sodium and chloride ions

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5T1F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	Tacsimate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.119	α = 90
b = 109.065	β = 98.83
c = 95.017	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	IMAGE PLATE	RIGAKU RAXIS VII		2016-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.8	19.64	96	0.08	0.08	6.6	3.58		80576

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	1.8	1.86	93.3		0.514	1.8	3.54

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5T1F	1.8	19.64	76559	4016	95.95	0.212	0.2092	0.21	0.2657	0.26	RANDOM	32.891

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.333
r_dihedral_angle_4_deg	19.802
r_dihedral_angle_3_deg	16.612
r_dihedral_angle_1_deg	8.379
r_angle_refined_deg	0.858
r_angle_other_deg	0.527
r_chiral_restr	0.056
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.333
r_dihedral_angle_4_deg	19.802
r_dihedral_angle_3_deg	16.612
r_dihedral_angle_1_deg	8.379
r_angle_refined_deg	0.858
r_angle_other_deg	0.527
r_chiral_restr	0.056
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6660
Nucleic Acid Atoms
Solvent Atoms	763
Heterogen Atoms	123

Software

Software
Software Name	Purpose
CrystalClear	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
d*TREK	data scaling
CrystalClear	data reduction

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 R01GM157729.