8RP0 | pdb_00008rp0

Aminodeoxychorismate synthase complex from Escherichia coli, with glutamine and chorismate added

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	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.184	α = 90
b = 109.946	β = 90
c = 175.619	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)	0.9762	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	1.64	46.639	99.97	0.1203	0.997	11.21	13.2		189833

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	1.64	1.699	99.99		1.797	0.677	1.21	13.3

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	1.64	46.639	189833	9423	99.983	0.171	0.1696	0.1697	0.1992	0.1996	33.526

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]
-0.824			1.706		-0.882

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.758
r_dihedral_angle_4_deg	17.143
r_dihedral_angle_3_deg	13.998
r_lrange_it	7.607
r_lrange_other	7.561
r_dihedral_angle_1_deg	7.4
r_scangle_it	6.052
r_scangle_other	6.045
r_scbond_it	4.193
r_scbond_other	4.189
r_mcangle_it	4.014
r_mcangle_other	4.014
r_dihedral_angle_other_2_deg	3.142
r_mcbond_it	2.961
r_mcbond_other	2.96
r_angle_refined_deg	1.667
r_angle_other_deg	1.417
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.213
r_nbd_other	0.209
r_symmetry_nbd_refined	0.194
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.141
r_ncsr_local_group_1	0.133
r_symmetry_xyhbond_nbd_other	0.13
r_ncsr_local_group_2	0.096
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10145
Nucleic Acid Atoms
Solvent Atoms	999
Heterogen Atoms	142

Software

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