9HJ5 | pdb_00009hj5

Engineered Fructosyl Peptide Oxidase - D7 mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277.15	12% PEG 8K, 5% Ethanol, 0.1M Tris-HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.51	43.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.083	α = 80.071
b = 54.12	β = 85.533
c = 82.657	γ = 89.837

Symmetry
Space Group	P 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 EIGER2 XE 16M		2024-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.093	53.974	96.89	0.982	5.2	3.2		52616

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.093	2.129			0.357

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FREE R-VALUE	2.093	53.974	52616	2614	96.913	0.196	0.1928	0.193	0.2571	0.2571	41.645

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]
-0.093	-0.435	0.058	-0.465	0.233	0.601

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.231
r_dihedral_angle_6_deg	15.084
r_dihedral_angle_2_deg	9.841
r_lrange_it	8.236
r_lrange_other	8.178
r_dihedral_angle_1_deg	7.82
r_scangle_it	5.918
r_scangle_other	5.917
r_mcangle_it	5.383
r_mcangle_other	5.383
r_scbond_it	3.985
r_scbond_other	3.985
r_mcbond_it	3.77
r_mcbond_other	3.766
r_angle_refined_deg	1.519
r_angle_other_deg	0.533
r_symmetry_nbd_refined	0.271
r_symmetry_xyhbond_nbd_refined	0.235
r_nbd_refined	0.23
r_symmetry_nbd_other	0.205
r_xyhbond_nbd_refined	0.198
r_nbtor_refined	0.186
r_nbd_other	0.153
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.034
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6514
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	136

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
REFMAC	phasing