7FTA | pdb_00007fta

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z228589380

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8BLU	8BLU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	100 mM Morpheus amino acids, 100 mM Morpheus buffer system 1, 43% Morpheus precipitant mix 3

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.181	α = 90
b = 49.712	β = 94.36
c = 115.736	γ = 90

Symmetry
Space Group	P 1 21 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		2022-08-08		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	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	2.03	57.67	99.8	0.09	0.098	0.037	0.991	10.5	6.9		59474

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	2.03	2.08	96.7		2.807	3.034	1.144	0.351		7	4204

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	8BLU	2.03	57.67	55235	2810	97.5	0.2481	0.2439	0.25	0.3295	0.33	RANDOM	60.69

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]
-1.33		0.07	-0.94		2.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.686
r_dihedral_angle_2_deg	10.279
r_mcangle_it	10.185
r_dihedral_angle_1_deg	8.377
r_mcbond_other	7.327
r_mcbond_it	7.326
r_angle_refined_deg	1.682
r_angle_other_deg	0.556
r_chiral_restr	0.072
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.686
r_dihedral_angle_2_deg	10.279
r_mcangle_it	10.185
r_dihedral_angle_1_deg	8.377
r_mcbond_other	7.327
r_mcbond_it	7.326
r_angle_refined_deg	1.682
r_angle_other_deg	0.556
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5908
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	99

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.