8EQ9 | pdb_00008eq9

Co-crystal structure of PERK with compound 11

X-RAY DIFFRACTION

---

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		277	12% PEG3350, 4% tacsimate pH7.0

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.728	α = 90
b = 126.728	β = 90
c = 58.769	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		2019-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00	APS	17-ID

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	2.86	55	100	0.126	8	9.6		12802

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	2.86	2.93			0.696

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	2.86	54.875	12763	648	99.517	0.241	0.239	0.28	0.2772	0.31	78.336

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]
-7.05	-3.525		-7.05		22.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.019
r_dihedral_angle_4_deg	18.21
r_dihedral_angle_3_deg	16.91
r_lrange_it	9.968
r_lrange_other	9.967
r_mcangle_other	7.165
r_mcangle_it	7.164
r_dihedral_angle_1_deg	6.95
r_scangle_it	5.826
r_scangle_other	5.824
r_mcbond_it	4.341
r_mcbond_other	4.339
r_scbond_it	3.386
r_scbond_other	3.385
r_angle_refined_deg	1.303
r_angle_other_deg	1.04
r_nbd_refined	0.208
r_symmetry_nbd_other	0.17
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.149
r_nbd_other	0.138
r_xyhbond_nbd_refined	0.129
r_symmetry_nbd_refined	0.075
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.047
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2090
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	30

Software

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