5QST | pdb_00005qst

PanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2447286438

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.598	α = 94.81
b = 72.046	β = 98.61
c = 118.412	γ = 115.22

Symmetry
Space Group	P 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		2018-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	2.58	60.55	98	0.064	0.091	0.064	0.991	5.8	1.8		59775

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	2.58	2.65	97.3		0.504	0.713	0.504	0.492		1.7	4403

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	6qb5	2.58	60.65	56804	2970	97.81	0.2323	0.2302	0.23	0.2713	0.27	RANDOM	85.573

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]
0.77	2.29	2.11	1.38	1.69	-6.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.969
r_dihedral_angle_4_deg	21.028
r_dihedral_angle_3_deg	20.226
r_dihedral_angle_1_deg	6.089
r_mcangle_it	3.721
r_mcbond_it	2.168
r_mcbond_other	2.168
r_angle_refined_deg	1.214
r_angle_other_deg	1.103
r_chiral_restr	0.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.969
r_dihedral_angle_4_deg	21.028
r_dihedral_angle_3_deg	20.226
r_dihedral_angle_1_deg	6.089
r_mcangle_it	3.721
r_mcbond_it	2.168
r_mcbond_other	2.168
r_angle_refined_deg	1.214
r_angle_other_deg	1.103
r_chiral_restr	0.048
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10033
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	15

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.