Experiment: 4WDI

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	20% PEG 3350, 0.2 M Sodium malonate, and 0.1 M Bis-Tris Propane, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.93	α = 68.11
b = 62.69	β = 85.79
c = 72.67	γ = 85.18

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 2M	mirrors	2012-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.917	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.313	29.518	90.2	0.068	0.12	0.081	8.6	2.1	30132	30132

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.31	2.37	91.5		0.351	0.351	0.43	2.2	2.2	2261

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.313	29.518	30131	1527	100	0.21	0.2061	0.2834	RANDOM	32.807

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]
1.01	-0.54	-0.1	0.25	1.46	-2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.718
r_dihedral_angle_4_deg	19.993
r_dihedral_angle_3_deg	18.666
r_dihedral_angle_1_deg	7.39
r_scangle_it	2.637
r_scbond_it	1.75
r_angle_refined_deg	1.598
r_mcangle_it	1.086
r_angle_other_deg	0.89
r_mcbond_it	0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.718
r_dihedral_angle_4_deg	19.993
r_dihedral_angle_3_deg	18.666
r_dihedral_angle_1_deg	7.39
r_scangle_it	2.637
r_scbond_it	1.75
r_angle_refined_deg	1.598
r_mcangle_it	1.086
r_angle_other_deg	0.89
r_mcbond_it	0.6
r_mcbond_other	0.135
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6388
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling
PHASER	phasing
GDA	data collection
GDA	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.