8PAJ | pdb_00008paj

Crystal Structure of a Squalene-Hopene cyclase from Archangium gephyra

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Deposition ID D_1292130979

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		292	0.1 M HEPES/MOPS [pH 7.5], 90 mM NaNO3, 90 mM Na2PO4, 90 mM (NH4)2SO4, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.958	α = 90
b = 84.165	β = 94.204
c = 87.968	γ = 90

Symmetry
Space Group	C 1 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	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	0.976284	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.46	43.87	100	0.103	0.997	9.2	6.2		117598

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.48	100		1.327	0.694	0.5

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	1.46	43.866	117014	5924	99.985	0.161	0.1591	0.16	0.1988	0.2	20.81

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]
-0.52		-0.29	0.321		0.239

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.063
r_dihedral_angle_3_deg	14.983
r_dihedral_angle_1_deg	5.819
r_dihedral_angle_2_deg	4.48
r_rigid_bond_restr	3.629
r_lrange_it	2.895
r_lrange_other	2.366
r_scangle_it	1.626
r_scangle_other	1.626
r_mcangle_it	1.62
r_mcangle_other	1.62
r_angle_refined_deg	1.539
r_scbond_it	1.19
r_scbond_other	1.19
r_mcbond_it	1.138
r_mcbond_other	1.138
r_angle_other_deg	0.835
r_nbd_refined	0.207
r_nbtor_refined	0.166
r_symmetry_nbd_other	0.144
r_symmetry_nbd_refined	0.138
r_xyhbond_nbd_refined	0.126
r_nbd_other	0.125
r_symmetry_xyhbond_nbd_refined	0.108
r_chiral_restr	0.092
r_ncsr_local_group_1	0.08
r_symmetry_nbtor_other	0.064
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5298
Nucleic Acid Atoms
Solvent Atoms	772
Heterogen Atoms	76

Software

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