3FJM | pdb_00003fjm

crystal structure of phosphate bound PEB3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HXW	PDB ENTRY 2hxw, PDB ENTRY peb3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	294	18% [w/v] polyethylene glycol 3350, 0.2 M sodium phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.417	α = 90
b = 79.965	β = 90
c = 98.392	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	MARRESEARCH	Vertical and Horizontal focusing Mirrors	2008-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID		APS	31-ID

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	1.6	18.7	98	0.067	15.8	6.6		65094			15

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)
	1.6	1.69	97.7		0.259	0.277	8.1	6.1	9228

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2hxw, PDB ENTRY peb3	1.6	18.7	61746	3261	99.05	0.21741	0.21667	0.23128	0.2433	RANDOM	13.385

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]
-0.56			0.63		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.333
r_dihedral_angle_3_deg	12.416
r_dihedral_angle_4_deg	9.981
r_dihedral_angle_1_deg	4.534
r_scangle_it	0.902
r_angle_refined_deg	0.798
r_scbond_it	0.523
r_mcangle_it	0.405
r_mcbond_it	0.212
r_chiral_restr	0.064
r_bond_refined_d	0.003
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3622
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	10

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
SCALA	data scaling