5JOS | pdb_00005jos

Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-3(P188L).

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	1 uL protein (18 mg/mL in 20 mM HEPES pH 7.5, 50 mM NaCl) + 1 uL precipitant (1.2 M sodium citrate, 50 mM TRIS pH 8.0).

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.37	α = 90
b = 90.37	β = 90
c = 101.81	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210r		2015-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	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	2.1	45.19	99.8	0.073	0.999	19.7	11.8		25229			36.1

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	2.1	2.16	98.2		0.76	2	5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3KBR	2.1	44.35	23894	1282	99.75	0.17715	0.17556	0.19	0.20679	0.21	RANDOM	48.698

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]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.451
r_dihedral_angle_4_deg	20.118
r_dihedral_angle_3_deg	15.517
r_long_range_B_refined	7.753
r_long_range_B_other	7.751
r_dihedral_angle_1_deg	6.6
r_scangle_other	5.9
r_scbond_other	4.026
r_scbond_it	4.023
r_mcangle_other	3.47
r_mcangle_it	3.455
r_mcbond_it	2.629
r_mcbond_other	2.598
r_angle_refined_deg	2.047
r_angle_other_deg	0.918
r_chiral_restr	0.125
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1928
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	23

Software

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