8CV8 | pdb_00008cv8

Structure of Hyoscyamine 6-beta Hydroxylase in complex with iron, 2-oxoglutarate, and hyoscyamine

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
2.16	43.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.851	α = 90
b = 79.25	β = 111.12
c = 56.019	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	CCD	RAYONIX MX-300		2020-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.53	50	100	0.076	0.03	0.996	24.2	7.5		54598

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	1.53	1.56	99.6		0.795	0.343	0.734	2.1

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	1.532	41.873	54598	2690	99.484	0.182	0.1812	0.1906	0.2077	0.2146	15.333

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]
-0.006		0.002	0.004		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.908
r_dihedral_angle_4_deg	11.928
r_dihedral_angle_3_deg	11.525
r_dihedral_angle_1_deg	6.624
r_lrange_it	3.596
r_lrange_other	3.595
r_scangle_it	1.712
r_scangle_other	1.711
r_mcangle_it	1.465
r_mcangle_other	1.465
r_angle_other_deg	1.24
r_angle_refined_deg	1.231
r_scbond_it	1.059
r_scbond_other	1.059
r_mcbond_it	0.828
r_mcbond_other	0.828
r_symmetry_nbd_refined	0.24
r_nbd_refined	0.198
r_symmetry_nbd_other	0.164
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.127
r_symmetry_metal_ion_refined	0.109
r_symmetry_xyhbond_nbd_refined	0.104
r_nbd_other	0.097
r_metal_ion_refined	0.076
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.059
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	2579
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	58

Software

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