8CQ3 | pdb_00008cq3

Bifunctional chorismate mutase/cyclohexadienyl dehydratase from Aequoribacter fuscus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CNZ	chorismate mutase from Burkholderia thailandesis
experimental model	PDB	5HPQ	cyclohexadienyl dehydratase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	0.1M Bis-TRIS propane, pH=7.5 0.2 M Sodium acetate 20% w/v PEG 3350 5 mg/mL protein in 20 mM TRIS-HCl, pH=8, 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.419	α = 90
b = 98.76	β = 108.519
c = 55.336	γ = 90

Symmetry
Space Group	P 1 21 1

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 PILATUS 2M		2021-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9655	ESRF	MASSIF-1

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	1.55	52.5	88.9	0.997	9.3	6.5		33225

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.73	69.7		0.529	1.6	6.9

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	1.55	52.47	33225	1578	61.729	0.2	0.1975	0.21	0.2511	0.25	24.704

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]
0.358		0.033	-0.22		-0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.574
r_dihedral_angle_6_deg	18.548
r_dihedral_angle_3_deg	17.873
r_dihedral_angle_1_deg	8.391
r_lrange_it	6.629
r_lrange_other	6.62
r_scangle_it	5.058
r_scangle_other	5.057
r_mcangle_it	3.812
r_mcangle_other	3.811
r_scbond_it	3.215
r_scbond_other	3.214
r_mcbond_it	2.509
r_mcbond_other	2.502
r_angle_refined_deg	1.575
r_angle_other_deg	0.518
r_symmetry_nbd_refined	0.249
r_nbd_refined	0.231
r_symmetry_xyhbond_nbd_refined	0.213
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.178
r_nbd_other	0.163
r_xyhbond_nbd_refined	0.16
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.077
r_chiral_restr_other	0.044
r_symmetry_xyhbond_nbd_other	0.044
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3079
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing