9SJI | pdb_00009sji

Crystal structure of SGBPdex (BT3088) with truncated residues 1-147

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		phenix.process_predicted_model to split by domain and run two simultaneous MR searches

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	MPD 1k 3350 35.5% w/v 200mM amino acid stock 100mM System 2 buffer (0.1M HEPES sodium salt and 0.1M MOPS at pH 7.5) pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.321	α = 90
b = 37.549	β = 100.345
c = 65.616	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 EIGER2 XE 16M		2021-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.89842	Diamond	I03

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	1.7	36.48	100	0.088	0.103	0.054	0.998	8	6.8		39600

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)
	1.7	1.73	100		2.063	2.424	1.264	0.713	0.7	7

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	1.7	36.477	39575	2011	99.929	0.202	0.1982	0.1983	0.27	0.2702	43.417

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]
-3.752		1.644	0.982		2.034

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	29.705
r_lrange_other	28.988
r_dihedral_angle_2_deg	21.183
r_dihedral_angle_3_deg	15.477
r_dihedral_angle_6_deg	14.571
r_scangle_it	8.555
r_scangle_other	8.553
r_dihedral_angle_1_deg	7.768
r_scbond_it	6.232
r_scbond_other	6.23
r_mcangle_other	6.031
r_mcangle_it	6.029
r_mcbond_it	4.876
r_mcbond_other	4.868
r_angle_refined_deg	2.214
r_angle_other_deg	0.899
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.149
r_nbd_other	0.143
r_symmetry_nbd_refined	0.139
r_chiral_restr	0.116
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_other	0.068
r_bond_refined_d	0.013
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2745
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
xia2	data scaling
Coot	model building
PHENIX	phasing
PHASER	phasing