Experiment: 4GVL

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LNQ	PDB ENTRY 1LNQ Gating Ring

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20-23% PEG3350, 120mM KCl, 80mM NaNO3, 1% Glycerol, 100mM Bis-Tris Propane, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.648	α = 90
b = 161.693	β = 90
c = 310.127	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	78	CCD	ADSC QUANTUM 315r		2008-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97924	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3	50					55435		1.829

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.07	93.6		1.8299	4.8	3440

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	PDB ENTRY 1LNQ Gating Ring	3	48.45	54224	1128	100	0.22886	0.22816	0.26178	RANDOM	124.639

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]
-0.29			-3.62		3.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.192
r_dihedral_angle_3_deg	20.389
r_dihedral_angle_4_deg	18.512
r_dihedral_angle_1_deg	5.905
r_scangle_it	1.34
r_angle_refined_deg	1.243
r_scbond_it	0.77
r_mcangle_it	0.627
r_mcbond_it	0.336
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.192
r_dihedral_angle_3_deg	20.389
r_dihedral_angle_4_deg	18.512
r_dihedral_angle_1_deg	5.905
r_scangle_it	1.34
r_angle_refined_deg	1.243
r_scbond_it	0.77
r_mcangle_it	0.627
r_mcbond_it	0.336
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.271
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.14
r_metal_ion_refined	0.102
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13840
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	100

Software

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

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.