Experiment: 4Q24

Crystal structure of Cyclo(L-leucyl-L-phenylalanyl) synthase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OQV	pdb entry 3OQV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	278	10%PEG8000, 50mM KCl, 50mM Na cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.968	α = 90
b = 86.968	β = 90
c = 70.738	γ = 120

Symmetry
Space Group	P 32 2 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	PSI PILATUS 6M		2012-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.984	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.9	37.7	98.1	0.079	11.45	2.71	7023	7023			80.89

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.07	98.5		0.606	1.75	2.72	1109

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3OQV	2.9	37.66	7001	7001	350	98.3	0.2034	0.2007	0.2526	0.2242	RANDOM	71.18

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]
0.0403			0.0403		-0.0807

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	22.11
t_omega_torsion	2.33
t_angle_deg	1.07
t_bond_d	0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1779
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	22

Software

Software
Software Name	Purpose
PHASER	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling