4FRO | pdb_00004fro

Crystal Structure of BBBB+UDP+Gal at pH 9.0 with MPD as the cryoprotectant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	298	1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM glycine, 30 mM sodium acetate with 20% MPD as cryoprotectant, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.164	α = 90
b = 150.737	β = 90
c = 79.182	γ = 90

Symmetry
Space Group	C 2 2 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	RAYONIX MX-300	9 CCDs, 9 TILED FIBER-OPTIC TAPERS	2012-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

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	1.7	40	96.7	0.057	14.9	4.8		33618

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	1.7	1.73	96.4		0.238		5.1	1650

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	3SXG	1.75	20	30772	1564	96.5	0.1854	0.1834	0.1827	0.2205	0.2186	RANDOM	24.7674

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]
-0.14			0.2		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.903
r_dihedral_angle_4_deg	18.426
r_dihedral_angle_3_deg	14.925
r_dihedral_angle_1_deg	6.715
r_angle_refined_deg	2.043
r_angle_other_deg	1.13
r_chiral_restr	0.125
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2265
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	43

Software

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