8CVB | pdb_00008cvb

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

X-RAY DIFFRACTION

---

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	42.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.801	α = 90
b = 79.329	β = 110.994
c = 55.848	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	99.9	0.046	0.018	0.93	34.8	7.6		54702

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		0.371	0.157	0.93	5	6.5

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	43.61	54702	2694	99.914	0.184	0.1826	0.1916	0.2037	0.2116	14.553

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]
0.001		-0.001	0.003		-0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.5
r_dihedral_angle_4_deg	12.667
r_dihedral_angle_3_deg	12.033
r_dihedral_angle_1_deg	6.59
r_lrange_it	4.17
r_lrange_other	3.937
r_scangle_it	1.372
r_scangle_other	1.372
r_mcangle_it	1.273
r_mcangle_other	1.272
r_angle_other_deg	1.201
r_angle_refined_deg	1.15
r_scbond_it	0.836
r_scbond_other	0.836
r_mcbond_it	0.706
r_mcbond_other	0.705
r_symmetry_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.199
r_nbd_refined	0.196
r_nbtor_refined	0.161
r_symmetry_nbd_other	0.16
r_nbd_other	0.124
r_xyhbond_nbd_refined	0.117
r_metal_ion_refined	0.076
r_symmetry_nbtor_other	0.074
r_symmetry_metal_ion_refined	0.074
r_chiral_restr	0.055
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	311
Heterogen Atoms	82

Software

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