7SMJ | pdb_00007smj

F2N structure, protein design with deep learning

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AI predicted model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	25% PEG 3350, 0.15 MgOAc, 0.1 Bis TRIS pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.13	α = 90
b = 48.72	β = 90
c = 75.58	γ = 90

Symmetry
Space Group	P 21 21 21

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	Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2	2021-01-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.58	37.79	99.9	0.05	0.051	1	32.23	33.017		24478			43.357

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.62	99.9		2.113	2.19	0.818	1.42	14.498

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	MOLECULAR REPLACEMENT	THROUGHOUT	AI predicted model	1.58	37.79	23254	1224	99.91	0.1779	0.1747	0.18	0.2379	0.24	RANDOM	50.026

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]
-0.73			-0.87		1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.827
r_dihedral_angle_4_deg	29.361
r_dihedral_angle_3_deg	15.178
r_rigid_bond_restr	6.379
r_dihedral_angle_1_deg	5.797
r_angle_refined_deg	1.535
r_angle_other_deg	1.426
r_chiral_restr	0.07
r_bond_refined_d	0.01
r_bond_other_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1322
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms

Software

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