8C2O | pdb_00008c2o

Structure of E. coli AmiA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	See paper for details.

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.515	α = 90
b = 73.899	β = 90
c = 115.563	γ = 90

Symmetry
Space Group	P 2 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	PIXEL	DECTRIS EIGER X 16M		2021-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.97950	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.35	59.6	100	0.05	0.999	10.4	12.6		21955			51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43	100		0.506	0.662	1.5	12.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.35	59.586	21893	1074	99.89	0.18	0.177	0.18	0.236	0.24	53.965

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]
-1.445			-0.646		2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.701
r_dihedral_angle_6_deg	15.196
r_lrange_other	11.163
r_lrange_it	11.15
r_scangle_it	9.071
r_scangle_other	9.069
r_mcangle_it	7.151
r_mcangle_other	7.15
r_dihedral_angle_2_deg	6.737
r_dihedral_angle_1_deg	6.443
r_scbond_it	6.164
r_scbond_other	6.162
r_mcbond_it	5.077
r_mcbond_other	5.06
r_angle_refined_deg	1.433
r_angle_other_deg	0.474
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.213
r_nbd_other	0.195
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.17
r_ncsr_local_group_1	0.105
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_refined	0.074
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3498
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing