8CVD | pdb_00008cvd

Structure of Hyoscyamine 6-beta Hydroxylase in complex with iron, succinate, and scopolamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TTM	6TTM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG 3350, sodium formate, strontium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.796	α = 90
b = 79.214	β = 111.24
c = 55.957	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 EIGER X 16M		2021-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03317	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.717	50	98.1	0.127	0.054	0.988	17.5	6.1		37388

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.717	1.75	97.5		1.098	0.599	0.536	1.7	4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6TTM	1.717	43.599	37388	1770	96.002	0.182	0.1816	0.1913	0.1991	0.2083	20.502

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]
-0.003			-0.001		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.968
r_dihedral_angle_4_deg	12.622
r_dihedral_angle_3_deg	12.475
r_dihedral_angle_1_deg	6.692
r_lrange_it	3.749
r_lrange_other	3.652
r_scangle_other	2.158
r_scangle_it	2.157
r_mcangle_it	1.783
r_mcangle_other	1.782
r_scbond_it	1.3
r_scbond_other	1.294
r_angle_refined_deg	1.217
r_angle_other_deg	1.19
r_mcbond_it	1.04
r_mcbond_other	1.039
r_nbd_refined	0.204
r_symmetry_nbd_other	0.164
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.137
r_xyhbond_nbd_refined	0.129
r_nbd_other	0.125
r_metal_ion_refined	0.121
r_symmetry_metal_ion_refined	0.078
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.058
r_symmetry_xyhbond_nbd_refined	0.04
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2578
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing