Experiment: 5XDT

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	293	100mM Tris-HCl, 41% w/v PEP629, 300mM KCl

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.553	α = 90
b = 51.193	β = 108.68
c = 86.449	γ = 90

Symmetry
Space Group	C 1 2 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	RAYONIX MX300HE		2016-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.900	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.3	50	99.5	0.049	0.053	0.02	8.6	7		71548

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	1.3	1.32	100		0.76	0.823	0.311	0.841		6.9	3620

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	pdbid 3VOA	1.3	40.95	68064	3484	99.38	0.1377	0.1361	0.1681	RANDOM	25.435

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.926
r_sphericity_free	35.363
r_dihedral_angle_3_deg	13.191
r_sphericity_bonded	12.581
r_dihedral_angle_4_deg	11.583
r_rigid_bond_restr	11.365
r_dihedral_angle_1_deg	5.621
r_angle_other_deg	3.643
r_angle_refined_deg	1.746
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.926
r_sphericity_free	35.363
r_dihedral_angle_3_deg	13.191
r_sphericity_bonded	12.581
r_dihedral_angle_4_deg	11.583
r_rigid_bond_restr	11.365
r_dihedral_angle_1_deg	5.621
r_angle_other_deg	3.643
r_angle_refined_deg	1.746
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2211
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL	data reduction

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 R01GM133198.