Experiment: 4WVE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TIP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M magnesium chloride, 0.1 M HEPES, 30% PEG400, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.861	α = 84.76
b = 45.628	β = 83.22
c = 60.359	γ = 78.6

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 6M-F		2014-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	59.79	98.9	0.089	0.05	0.992	15.8	4.3		53868			14.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	97.9		0.511	0.278	0.929	4.6	4.3	2631

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	FREE R-VALUE	3TIP	1.6	59.79	50959	2694	98.47	0.2093	0.2071	0.249	RANDOM	25.569

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]
1.79	0.42	0.05	-0.28	1.2	-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.102
r_dihedral_angle_4_deg	18.902
r_dihedral_angle_3_deg	12.539
r_dihedral_angle_1_deg	6.053
r_mcangle_it	2.007
r_angle_refined_deg	1.725
r_mcbond_other	1.347
r_mcbond_it	1.346
r_angle_other_deg	1.115
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.102
r_dihedral_angle_4_deg	18.902
r_dihedral_angle_3_deg	12.539
r_dihedral_angle_1_deg	6.053
r_mcangle_it	2.007
r_angle_refined_deg	1.725
r_mcbond_other	1.347
r_mcbond_it	1.346
r_angle_other_deg	1.115
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3170
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	1

Software

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