Experiment: 3VWI

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	20% Jeffamine, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.17	α = 90
b = 44.29	β = 92.8
c = 114.71	γ = 90

Symmetry
Space Group	P 1 21 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 210	Collimating and focusing mirrors: Rhodium coated silicon single crystals	2012-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.000	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.7	114.573	93.7	0.068	0.068	12.8	3.5	80105	80105		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	75.1		0.291	0.291	0.348	0.188	2.6	2.9	9190

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	3LIM	1.7	114.57	80105	80105	3182	93.29	0.1549	0.1549	0.1533	0.16	0.1936	0.2	RANDOM	19.4017

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]
-1.1		-0.03	0.32		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.216
r_dihedral_angle_4_deg	13.891
r_dihedral_angle_3_deg	13.604
r_dihedral_angle_1_deg	6.961
r_angle_refined_deg	1.954
r_chiral_restr	0.159
r_bond_refined_d	0.02
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5536
Nucleic Acid Atoms
Solvent Atoms	722
Heterogen Atoms	32

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

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.