6YMZ | pdb_00006ymz

Structure of the CheB methylsterase from P. atrosepticum SCRI1043

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A2O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION		293	2.0M NH4 Sulphate,0.1M Tris-HCl pH 8.50 // 1.25M Na Citrate, 0.1M Na-Hepes pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.741	α = 90
b = 148.741	β = 90
c = 206.34	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2019-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9791	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.3	63.31	98.44	0.826	40.01	26.2		98138			31.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.382	98.13		0.649	3.41	25.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1a2o	2.3	63.31	1.34	97531	4877	98.45	0.1935	0.1919	0.19	0.2261	0.23	43.93

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.0517
f_angle_d	0.6978
f_chiral_restr	0.0455
f_plane_restr	0.0047
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12787
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	59

Software

Software
Software Name	Purpose
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
Coot	model building