Experiment: 3GVT

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	0.2M ammonium citrate, 0.2M Li2SO4, 22%(w/v) PEG 4000 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.54	α = 90
b = 150.54	β = 90
c = 77.22	γ = 120

Symmetry
Space Group	P 63

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 315		2008-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.92	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.8	37.88	99.9	0.089	11.5	5.4	24770	24746		5.7	75.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	100		0.471	5.7	5.5	3595

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3GVO	2.8	37.87	23492	23335	1250	99.33	0.19457	0.19457	0.19151	0.25317	RANDOM	63.549

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]
0.19	0.09		0.19		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.121
r_dihedral_angle_4_deg	20.462
r_dihedral_angle_3_deg	17.3
r_dihedral_angle_1_deg	4.904
r_scangle_it	2.168
r_angle_refined_deg	1.328
r_scbond_it	1.29
r_mcangle_it	0.935
r_mcbond_it	0.53
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.121
r_dihedral_angle_4_deg	20.462
r_dihedral_angle_3_deg	17.3
r_dihedral_angle_1_deg	4.904
r_scangle_it	2.168
r_angle_refined_deg	1.328
r_scbond_it	1.29
r_mcangle_it	0.935
r_mcbond_it	0.53
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.23
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5552
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	20

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.