Experiment: 1VGJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IUH	PDB entry 1iuh

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	Ammonium acetate, Sodium acetate, PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.5	α = 90
b = 45.7	β = 90
c = 97.6	γ = 90

Symmetry
Space Group	P 21 21 21

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		2004-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	0.97950	SPring-8	BL44B2

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	1.94	50	99.9	0.047	0.047	16.5	7	14330	14330		-3	50.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.94	2.01	99.6		0.384	0.384		6.6	1394

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1iuh	1.94	10	14194	12780	1414	100	0.21584	0.21047	0.26487	RANDOM	33.802

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]
1.29			-0.99		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	7.231
r_dihedral_angle_1_deg	5.898
r_scbond_it	4.291
r_mcangle_it	2.848
r_angle_refined_deg	1.966
r_mcbond_it	1.602
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.212
r_chiral_restr	0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	7.231
r_dihedral_angle_1_deg	5.898
r_scbond_it	4.291
r_mcangle_it	2.848
r_angle_refined_deg	1.966
r_mcbond_it	1.602
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.212
r_chiral_restr	0.156
r_symmetry_hbond_refined	0.143
r_bond_refined_d	0.027
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1488
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.