8CVA | pdb_00008cva

Structure of Hyoscyamine 6-beta Hydroxylase in complex with iron, succinate, and 6-OH-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	42.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.839	α = 90
b = 79.258	β = 111.22
c = 55.96	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 PILATUS3 6M		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	1.58	50	98.6	0.086	0.036	0.997	20.1	6.3		48707

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	1.58	1.61	98.7		0.675	0.364	0.697	2.3	4.1

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	1.581	43.613	48707	2534	97.635	0.186	0.1853	0.1955	0.2055	0.2146	14.871

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]
-0.004			0.005		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.319
r_dihedral_angle_4_deg	13.518
r_dihedral_angle_3_deg	11.896
r_dihedral_angle_1_deg	6.489
r_lrange_it	3.421
r_lrange_other	3.254
r_scangle_it	1.48
r_scangle_other	1.479
r_mcangle_it	1.344
r_mcangle_other	1.343
r_angle_other_deg	1.197
r_angle_refined_deg	1.17
r_scbond_it	0.899
r_scbond_other	0.898
r_mcbond_it	0.749
r_mcbond_other	0.749
r_nbd_refined	0.198
r_symmetry_nbd_refined	0.19
r_symmetry_nbd_other	0.162
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.131
r_symmetry_metal_ion_refined	0.13
r_nbd_other	0.122
r_symmetry_xyhbond_nbd_refined	0.099
r_metal_ion_refined	0.086
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.056
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
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	265
Heterogen Atoms	70

Software

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