Experiment: 3VI6

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.3M potassium chrolide, 1mM EDTA, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.282	α = 90
b = 56.282	β = 90
c = 203.628	γ = 120

Symmetry
Space Group	H 3 2

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	crystals	2010-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.000	Photon Factory	AR-NW12A

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	1.59	50	99.6	0.052	39	10.7		16978			17.9

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	1.59	1.62	98.3		0.31	8.2	10.1	814

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 1NUM	1.59	50	16106	864	99.48	0.19114	0.18985	0.21625	RANDOM	19.046

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]
0.79	0.39		0.79		-1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	31.54
r_dihedral_angle_2_deg	26.477
r_dihedral_angle_3_deg	13.146
r_dihedral_angle_1_deg	4.774
r_scangle_it	4.484
r_scbond_it	2.909
r_mcangle_it	1.632
r_rigid_bond_restr	1.25
r_angle_refined_deg	1.157
r_mcbond_it	0.852

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	31.54
r_dihedral_angle_2_deg	26.477
r_dihedral_angle_3_deg	13.146
r_dihedral_angle_1_deg	4.774
r_scangle_it	4.484
r_scbond_it	2.909
r_mcangle_it	1.632
r_rigid_bond_restr	1.25
r_angle_refined_deg	1.157
r_mcbond_it	0.852
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	753
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	3

Software

Software
Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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.