Experiment: 3GF4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BI8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	5 mg/mL protein, 85 mM ammonium acetate, 42 mM tri-sodium citrate, 12.3% PEG 4000, 7.5% glycerol, 15 mM L-cysteine, 5 mM UDP-Glc, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.951	α = 90
b = 93.951	β = 90
c = 130.259	γ = 90

Symmetry
Space Group	P 41

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	rhodium coated toroidal mirror	2006-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	0.9002	APS	14-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.45	50	98.6	0.11	14.831	4.9	41757	41161			53.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.45	2.54	97		0.366	4.2	4.9	4042

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	2BI8	2.45	30	41510	40988	2064	98.74	0.194	0.194	0.192	0.238	RANDOM	45.792

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]
-1.79			-1.79		3.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.225
r_dihedral_angle_4_deg	19.512
r_dihedral_angle_3_deg	16.612
r_dihedral_angle_1_deg	6.663
r_scangle_it	3.974
r_scbond_it	2.857
r_angle_refined_deg	1.712
r_mcangle_it	1.698
r_mcbond_it	1.466
r_nbtor_refined	0.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.225
r_dihedral_angle_4_deg	19.512
r_dihedral_angle_3_deg	16.612
r_dihedral_angle_1_deg	6.663
r_scangle_it	3.974
r_scbond_it	2.857
r_angle_refined_deg	1.712
r_mcangle_it	1.698
r_mcbond_it	1.466
r_nbtor_refined	0.322
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.18
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.117
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6238
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	163

Software

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