8PAK

Crystal Structure of a Squalene-Hopene Cyclase from Cystobacter fuscus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	RoseTTAFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.5	292	0.1 M Bicine/Trizma base pH 8.5, 0.03 M MgCl2, 0.03 M CaCl2, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.244	α = 90
b = 75.872	β = 94.269
c = 91.742	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 EIGER2 X 16M		2021-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.42	58.42	97.89	0.129	0.142	0.057	0.993	6.9	6.4		121895

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.44	95.59		1.877	2.035	0.776	0.343	0.5	7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.42	45.785	121524	6103	97.838	0.168	0.1661	0.2049	13.039

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]
2.342		0.029	-0.762		-1.567

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.524
r_dihedral_angle_3_deg	13.462
r_dihedral_angle_2_deg	7.992
r_dihedral_angle_1_deg	5.846
r_rigid_bond_restr	3.381
r_lrange_it	2.126
r_lrange_other	1.956
r_angle_refined_deg	1.513
r_mcangle_it	1.203
r_mcangle_other	1.203
r_scangle_it	1.182
r_scangle_other	1.182
r_mcbond_it	0.845
r_mcbond_other	0.844
r_scbond_it	0.844
r_scbond_other	0.844
r_angle_other_deg	0.638
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.187
r_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.181
r_symmetry_nbd_other	0.173
r_xyhbond_nbd_refined	0.131
r_ncsr_local_group_1	0.129
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.071
r_symmetry_xyhbond_nbd_other	0.057
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5371
Nucleic Acid Atoms
Solvent Atoms	714
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MrBUMP	phasing