8EQD | pdb_00008eqd

Co-crystal structure of PERK with compound 24

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, HANGING DROP		277	100 mM HEPES pH 7.0, 180 mM Na/K tartrate, 9% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.9	α = 90
b = 125.9	β = 90
c = 55.216	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		2019-06-11	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)	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	2.92	41.51	95.3	0.097	0.997	9.5	6.7		10640

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	2.92	2.97			0.794	0.817

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	2.92	41.51	10631	509	95.149	0.248	0.246	0.3	0.2796	0.31	93.984

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]
-8.076	-4.038		-8.076		26.199

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.157
r_dihedral_angle_4_deg	16.193
r_dihedral_angle_3_deg	15.414
r_lrange_it	8.277
r_lrange_other	8.275
r_dihedral_angle_1_deg	5.771
r_mcangle_it	5.499
r_mcangle_other	5.497
r_scangle_it	4.06
r_scangle_other	4.059
r_mcbond_it	3.093
r_mcbond_other	3.082
r_scbond_it	2.128
r_scbond_other	2.127
r_angle_refined_deg	1.21
r_angle_other_deg	0.979
r_symmetry_nbd_refined	0.209
r_nbd_other	0.184
r_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.176
r_symmetry_nbd_other	0.161
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.144
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.035
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2106
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	31

Software

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