8EQE | pdb_00008eqe

Co-crystal structure of PERK with compound 26

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4X7J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	4% tacsimate pH 7.0 and 12% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.342	α = 90
b = 125.342	β = 90
c = 58.084	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		2019-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.559	54.275	100	0.072	15	9.7		17214

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	2.559	2.63			1.18

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	MOLECULAR REPLACEMENT	FREE R-VALUE	4X7J	2.559	54.275	17195	883	99.866	0.227	0.2242	0.24	0.2873	0.24	78.053

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]
-4.949	-2.474		-4.949		16.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.007
r_dihedral_angle_3_deg	16.925
r_dihedral_angle_4_deg	15.016
r_lrange_it	8.772
r_lrange_other	8.77
r_mcangle_other	6.527
r_mcangle_it	6.526
r_dihedral_angle_1_deg	6.411
r_scangle_it	5.52
r_scangle_other	5.518
r_mcbond_it	3.893
r_mcbond_other	3.891
r_scbond_it	3.132
r_scbond_other	3.131
r_angle_refined_deg	1.249
r_angle_other_deg	1.055
r_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.169
r_nbtor_refined	0.165
r_nbd_other	0.162
r_xyhbond_nbd_refined	0.134
r_symmetry_nbd_refined	0.097
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.043
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2108
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	34

Software

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