Experiment: 6CD8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CCR	early version of PDB entry 6ccr

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	30% PEG2000 and 0.1M KSCN

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.941	α = 90
b = 63.941	β = 90
c = 289.593	γ = 120

Symmetry
Space Group	P 65 2 2

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 PILATUS3 6M		2017-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97945	APS	19-ID

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	1.6	48.27	100	0.059	0.061	0.014	1	26.9	19.1		47911

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	1.6	1.63	99.7		1.638	1.681	0.373	0.803		19.8	2379

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	early version of PDB entry 6ccr	1.6	48.2	45300	2382	99.99	0.1982	0.1969	0.21	0.2237	0.24	30.639

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]
-0.06	-0.03		-0.06		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.119
r_dihedral_angle_4_deg	16.958
r_dihedral_angle_3_deg	11.662
r_dihedral_angle_1_deg	7.135
r_angle_refined_deg	1.619
r_mcangle_it	1.303
r_angle_other_deg	0.946
r_mcbond_it	0.826
r_mcbond_other	0.824
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.119
r_dihedral_angle_4_deg	16.958
r_dihedral_angle_3_deg	11.662
r_dihedral_angle_1_deg	7.135
r_angle_refined_deg	1.619
r_mcangle_it	1.303
r_angle_other_deg	0.946
r_mcbond_it	0.826
r_mcbond_other	0.824
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2741
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	19

Software

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