6ZK0 | pdb_00006zk0

1.47A human IMPase with ebselen

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GJ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.2M MnS04, 0.1M MES, 28% PEG4000 and pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.02	α = 90
b = 84.02	β = 90
c = 150.22	γ = 120

Symmetry
Space Group	P 32 2 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 PILATUS 6M-F		2019-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91188	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.47	24.44	100	0.053	0.022	1	20.4	11		104886

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	1.47	1.5			2.019	2.123	0.652	0.498	1.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	6gj0	1.47	24.438	104821	5081	99.966	0.181	0.1791	0.18	0.2083	0.21	30.088

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]
-0.032	-0.016		-0.032		0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.5
r_dihedral_angle_4_deg	14.469
r_dihedral_angle_3_deg	13.783
r_dihedral_angle_1_deg	8.411
r_lrange_it	6.854
r_scangle_it	5.276
r_scbond_it	3.84
r_mcangle_it	3.536
r_mcbond_it	2.567
r_angle_refined_deg	1.901
r_metal_ion_refined	0.359
r_nbtor_refined	0.323
r_xyhbond_nbd_refined	0.276
r_nbd_refined	0.241
r_symmetry_nbd_refined	0.239
r_symmetry_xyhbond_nbd_refined	0.235
r_chiral_restr	0.14
r_symmetry_metal_ion_refined	0.109
r_bond_refined_d	0.011
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4106
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms	122

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing