9KEK | pdb_00009kek

human glyoxalase I (with C-ter His tag) in complex with piceatannol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7WT2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.2 M Sodium chloride, 0.1 M Bis-Tris, 25%(w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.956	α = 90
b = 65.758	β = 96.218
c = 69.633	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 4M		2024-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.018	Photon Factory	BL-1A

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	2.11	19.93	100	0.089	0.993	16.8	3.5		38343

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	2.11	2.15	100		0.317	0.911	4.1	3.6

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	THROUGHOUT	2.11	19.93	38316	1897	99.758	0.17	0.1664	0.1682	0.2328	0.2336	26.764

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]
2.69		-0.865	-1.258		-1.214

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.282
r_dihedral_angle_3_deg	16.982
r_dihedral_angle_6_deg	15.472
r_lrange_other	9
r_lrange_it	8.995
r_dihedral_angle_1_deg	7.202
r_scangle_it	7.128
r_scangle_other	7.127
r_mcangle_other	5.139
r_mcangle_it	5.138
r_scbond_it	5.118
r_scbond_other	5.117
r_mcbond_it	3.716
r_mcbond_other	3.711
r_angle_refined_deg	2.345
r_angle_other_deg	0.791
r_nbd_other	0.302
r_symmetry_nbd_refined	0.274
r_nbd_refined	0.216
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.186
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.118
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_metal_ion_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5636
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	110

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing