6SLB | pdb_00006slb

Crystal structure of isomerase PaaG with trans-3,4-didehydroadipyl-CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HRX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	50 mM KH2PO4, pH 4.5, 20-22% PEG 3350, 3% (w/v) NDSB-201 and 20% glycerol (v/v)

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.024	α = 90
b = 88.024	β = 90
c = 88.024	γ = 90

Symmetry
Space Group	P 21 3

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		2019-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.88	44.01	99.41	0.997	22.48	2		18671

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.947			0.2998

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3HRX	1.88	44.01	18665	1013	99.419	0.171	0.1681	0.18	0.2171	0.22	35.196

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.763
r_dihedral_angle_4_deg	15.151
r_dihedral_angle_3_deg	14.714
r_lrange_other	7.308
r_lrange_it	7.301
r_dihedral_angle_1_deg	6.878
r_scangle_it	6.054
r_scangle_other	6.052
r_scbond_it	4.075
r_scbond_other	4.073
r_mcangle_other	3.755
r_mcangle_it	3.753
r_mcbond_it	2.901
r_mcbond_other	2.891
r_chiral_restr_other	2.118
r_angle_refined_deg	1.705
r_angle_other_deg	1.546
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.198
r_symmetry_nbd_other	0.187
r_nbd_other	0.182
r_symmetry_xyhbond_nbd_other	0.169
r_symmetry_xyhbond_nbd_refined	0.157
r_nbtor_refined	0.156
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.011
r_xyhbond_nbd_other	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1960
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	57

Software

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