8PBO | pdb_00008pbo

Deep interactome learning for generative drug design

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AWC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	1.6 M Ammoniumsulphate, 0.1 M Tris/HCl pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.413	α = 90
b = 60.611	β = 102.859
c = 117.945	γ = 90

Symmetry
Space Group	C 1 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 EIGER X 16M		2023-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	44.28	100	0.999	17.1	7		55065

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89			0.903

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.85	44.28	55064	2778	99.989	0.173	0.1707	0.18	0.2128	0.22	46.811

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]
-1.437		1.29	1.965		-1.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.657
r_dihedral_angle_6_deg	16.162
r_lrange_it	10.206
r_lrange_other	10.206
r_dihedral_angle_2_deg	9.025
r_scangle_it	8.842
r_scangle_other	8.762
r_scbond_it	6.215
r_scbond_other	6.165
r_mcangle_other	5.92
r_mcangle_it	5.919
r_dihedral_angle_1_deg	5.554
r_mcbond_it	4.573
r_mcbond_other	4.573
r_angle_refined_deg	2.1
r_angle_other_deg	0.674
r_nbd_refined	0.239
r_symmetry_nbd_refined	0.211
r_nbtor_refined	0.195
r_symmetry_nbd_other	0.191
r_nbd_other	0.179
r_ncsr_local_group_1	0.159
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.133
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4236
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	79

Software

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