Experiment: 6SCD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SBN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		285	0.2 M ammonium sulphate, 0.1 M sodium citrate pH 3.5, 28 % (v/v) PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.526	α = 90
b = 98.268	β = 90
c = 121.233	γ = 90

Symmetry
Space Group	I 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		2019-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.950500	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.35	77	99.1	0.043	14.98	4.05		122029

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.42			0.439

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6SBN	1.35	76.34	116011	6011	99.11	0.1146	0.1127	0.1517	RANDOM	21.684

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]
-0.13			0.38		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.352
r_dihedral_angle_2_deg	29.813
r_dihedral_angle_4_deg	15.41
r_sphericity_bonded	15.367
r_dihedral_angle_3_deg	11.22
r_dihedral_angle_1_deg	6.725
r_rigid_bond_restr	5.799
r_angle_refined_deg	2.43
r_angle_other_deg	1.336
r_chiral_restr	0.149

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.352
r_dihedral_angle_2_deg	29.813
r_dihedral_angle_4_deg	15.41
r_sphericity_bonded	15.367
r_dihedral_angle_3_deg	11.22
r_dihedral_angle_1_deg	6.725
r_rigid_bond_restr	5.799
r_angle_refined_deg	2.43
r_angle_other_deg	1.336
r_chiral_restr	0.149
r_bond_refined_d	0.026
r_gen_planes_refined	0.015
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3995
Nucleic Acid Atoms
Solvent Atoms	493
Heterogen Atoms	49

Software

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