7JJN | pdb_00007jjn

Eubacterium rectale Amy13B (EUR_01860)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.17M Am Sulfate, 25.5% PEG 4000, 15% glycerol (JCSG+ screen, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.18	α = 90
b = 82.76	β = 92.86
c = 85.86	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER X 9M		2016-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.979	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.25	38.07	99	0.15	0.16	0.99	9.9	7		55448

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.33	99.5		0.84	0.77		7.2

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	1WZA	2.25	38.07	52665	2783	98.95	0.1639	0.1621	0.1984	0.1789	RANDOM	34.396

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]
-0.49		0.86	0.63		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.077
r_dihedral_angle_4_deg	16.89
r_dihedral_angle_3_deg	14.481
r_dihedral_angle_1_deg	6.402
r_angle_refined_deg	1.108
r_angle_other_deg	0.839
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8144
Nucleic Acid Atoms
Solvent Atoms	543
Heterogen Atoms	100

Software

Software
Software Name	Purpose
xia2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction