8CVE | pdb_00008cve

Structure of L289F 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
2.15	42.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.763	α = 90
b = 79.215	β = 111.053
c = 55.757	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		2020-10-16	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	1.53	50	96.6	0.089	0.04	0.995	22.1	5.5		52325

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	89.4		0.451	0.238	0.863	4.2	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	1.53	43.529	52325	2572	95.578	0.185	0.1845	0.1947	0.2043	0.2137	14.197

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		0.002	-0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.276
r_dihedral_angle_4_deg	12.547
r_dihedral_angle_3_deg	11.584
r_dihedral_angle_1_deg	6.567
r_lrange_it	3.83
r_lrange_other	3.501
r_scangle_it	1.265
r_scangle_other	1.265
r_angle_refined_deg	1.2
r_mcangle_it	1.191
r_mcangle_other	1.19
r_angle_other_deg	1.189
r_scbond_other	0.778
r_scbond_it	0.777
r_mcbond_it	0.66
r_mcbond_other	0.66
r_nbd_refined	0.194
r_symmetry_nbd_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.179
r_symmetry_nbd_other	0.163
r_nbtor_refined	0.16
r_nbd_other	0.121
r_xyhbond_nbd_refined	0.115
r_metal_ion_refined	0.111
r_symmetry_metal_ion_refined	0.103
r_symmetry_nbtor_other	0.075
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	2572
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	67

Software

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