7GAE | pdb_00007gae

PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with Z1688504114

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.7	293	36% PEG 8000, 0.1M acetate pH 4.7

Crystal Properties
Matthews coefficient	Solvent content
2.24	44.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.917	α = 90
b = 60.917	β = 90
c = 35.653	γ = 90

Symmetry
Space Group	P 43

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		2023-02-08		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92124	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.92	43.08	99.8	0.113	0.118	0.032	0.999	11.6	13.6		10230

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	1.92	1.96	97.5		3.518	3.652	0.975	0.268		14.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	8Q53	1.92	43.11	9804	407	99.75	0.1994	0.1973	0.2169	0.2506	0.2677	RANDOM	50.216

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]
-0.52			-0.52		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.927
r_dihedral_angle_4_deg	21.757
r_dihedral_angle_3_deg	15.886
r_dihedral_angle_1_deg	6.453
r_mcangle_it	5.103
r_mcbond_it	3.446
r_mcbond_other	3.445
r_angle_refined_deg	1.594
r_angle_other_deg	1.206
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.927
r_dihedral_angle_4_deg	21.757
r_dihedral_angle_3_deg	15.886
r_dihedral_angle_1_deg	6.453
r_mcangle_it	5.103
r_mcbond_it	3.446
r_mcbond_other	3.445
r_angle_refined_deg	1.594
r_angle_other_deg	1.206
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	954
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	51

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.