7RSF | pdb_00007rsf

Acetylornithine deacetylase from Escherichia coli

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.1 M Bis-Tris Propane, 1 M ammonium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.7	α = 90
b = 70.994	β = 90
c = 289.884	γ = 90

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS3 X 6M		2021-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.13	46.15	98.8	0.12	0.133	0.057	0.986	6.2	4.9		54637

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.18	90.5		1.013	1.187	0.604	0.513	1.02	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.13	46.15	51807	2776	98.08	0.1899	0.1875	0.1947	0.2336	0.2361	RANDOM	46.425

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]
-2.07			2.45		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.234
r_dihedral_angle_4_deg	17.773
r_dihedral_angle_3_deg	16.21
r_dihedral_angle_1_deg	7.538
r_angle_refined_deg	1.617
r_angle_other_deg	1.313
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5917
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	15

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing