8RP6 | pdb_00008rp6

Aminodeoxychorismate synthase complex from Escherichia coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I7S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293.15	MES, magnesium sulfate heptahydrate, glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.505	α = 90
b = 108.326	β = 90
c = 179.758	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	PIXEL	DECTRIS EIGER X 16M		2021-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.968000	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.45	46.434	99.88	0.1465	0.998	11.91	13.4		57850

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	2.45	2.538	99.79		1.699	0.806	1.79	13.5

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	2.45	46.434	57849	2342	99.964	0.206	0.2042	0.2069	0.2537	0.2162	57.944

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]
-4.595			6.145		-1.551

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.985
r_dihedral_angle_3_deg	19.475
r_dihedral_angle_4_deg	17.557
r_lrange_other	11.605
r_lrange_it	11.603
r_scangle_it	7.386
r_scangle_other	7.385
r_dihedral_angle_1_deg	7.23
r_mcangle_it	6.309
r_mcangle_other	6.308
r_scbond_it	4.685
r_scbond_other	4.682
r_mcbond_it	4.185
r_mcbond_other	4.185
r_angle_refined_deg	1.504
r_angle_other_deg	1.269
r_symmetry_xyhbond_nbd_other	0.316
r_symmetry_nbd_refined	0.315
r_metal_ion_refined	0.292
r_nbd_other	0.242
r_symmetry_xyhbond_nbd_refined	0.214
r_nbd_refined	0.197
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.155
r_ncsr_local_group_1	0.126
r_ncsr_local_group_2	0.109
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
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	10128
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	55

Software

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