7FT8 | pdb_00007ft8

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with NCL-00024671

X-RAY DIFFRACTION

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
2.71	54.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.383	α = 90
b = 49.625	β = 95.42
c = 115.378	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	2.19	57.5	99.5	0.165	0.179	0.068	0.987	5.9	6.9		48094

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	2.19	2.26	94.4		2.61	2.834	1.093	0.344		6.6	4192

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	2.4	57.5	34641	1766	99.96	0.2237	0.2201	0.23	0.2914	0.29	RANDOM	63.484

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]
-3.49		3.44	-2.14		4.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.843
r_mcangle_it	8.343
r_dihedral_angle_1_deg	7.802
r_dihedral_angle_2_deg	6.035
r_mcbond_it	5.455
r_mcbond_other	5.447
r_angle_refined_deg	1.327
r_angle_other_deg	0.441
r_chiral_restr	0.058
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.843
r_mcangle_it	8.343
r_dihedral_angle_1_deg	7.802
r_dihedral_angle_2_deg	6.035
r_mcbond_it	5.455
r_mcbond_other	5.447
r_angle_refined_deg	1.327
r_angle_other_deg	0.441
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
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	232
Heterogen Atoms	101

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.