Experiment: 3VGD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EH9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	1.1M sodium citrate, 0.1M HEPES, 5mM MTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.881	α = 90
b = 78.881	β = 90
c = 282.53	γ = 120

Symmetry
Space Group	P 32 2 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	MAR CCD 165 mm	mirrors	2001-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

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	2.4	94.18	99.9	0.06	30.5	7.7		40919

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	2.4	2.49	99.9		0.179	5	6.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1EH9	2.4	61.5	40870	2050	99.93	0.1601	0.1581	0.16	0.1983	0.19	RANDOM	36.9521

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]
2.5	1.25		2.5		-3.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.656
r_dihedral_angle_3_deg	19.38
r_dihedral_angle_4_deg	18.112
r_dihedral_angle_1_deg	6.369
r_scangle_it	3.694
r_scbond_it	2.262
r_angle_refined_deg	1.537
r_mcangle_it	1.313
r_mcbond_it	0.66
r_chiral_restr	0.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.656
r_dihedral_angle_3_deg	19.38
r_dihedral_angle_4_deg	18.112
r_dihedral_angle_1_deg	6.369
r_scangle_it	3.694
r_scbond_it	2.262
r_angle_refined_deg	1.537
r_mcangle_it	1.313
r_mcbond_it	0.66
r_chiral_restr	0.137
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4537
Nucleic Acid Atoms
Solvent Atoms	392
Heterogen Atoms	43

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
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.