Experiment: 6AP7

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DNP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	Tris/Acetate 0.1M, MgCl2 0.2M, PEG 3350 27%

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.697	α = 82.67
b = 48.315	β = 86.76
c = 71.942	γ = 69.95

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	CCD	ADSC QUANTUM 210r		2015-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	MX1

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	1.51	45.08	95.9	0.084	0.098	0.049	0.998	12.1	4		69577			10.3

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	1.51	1.53	74.9		0.83	0.966	0.492	0.593		3.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	4DNP	1.51	36.27	66090	3485	95.87	0.1661	0.1644	0.18	0.1973	0.21	RANDOM	19.047

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]
-0.1	0.12	-0.09	-0.01	0.2	0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.059
r_dihedral_angle_4_deg	15.842
r_dihedral_angle_3_deg	13.102
r_dihedral_angle_1_deg	5.677
r_angle_refined_deg	1.76
r_angle_other_deg	1.436
r_chiral_restr	0.112
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_gen_planes_other	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.059
r_dihedral_angle_4_deg	15.842
r_dihedral_angle_3_deg	13.102
r_dihedral_angle_1_deg	5.677
r_angle_refined_deg	1.76
r_angle_other_deg	1.436
r_chiral_restr	0.112
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_gen_planes_other	0.01
r_bond_other_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4154
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	46

Software

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

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.