8CVH | pdb_00008cvh

Structure of L289F Hyoscyamine 6-beta Hydroxylase in complex with vanadyl, 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
2.17	43.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.915	α = 90
b = 79.102	β = 111.248
c = 56.276	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		2021-02-03	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	2.03	50	99.7	0.213	0.137	0.971	6.63	3.8		23863

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	2.03	2.07			1.715	1.102	0.118	0.82

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	2.03	43.752	22581	1200	95.002	0.203	0.2011	0.2093	0.2495	0.2508	24.662

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]
0.04			0.009		-0.038

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.682
r_dihedral_angle_3_deg	13.758
r_dihedral_angle_4_deg	11.797
r_dihedral_angle_1_deg	6.553
r_lrange_it	3.453
r_lrange_other	3.409
r_mcangle_it	1.893
r_mcangle_other	1.893
r_scangle_it	1.892
r_scangle_other	1.891
r_angle_refined_deg	1.187
r_angle_other_deg	1.108
r_mcbond_it	1.09
r_mcbond_other	1.089
r_scbond_it	1.086
r_scbond_other	1.085
r_symmetry_nbd_refined	0.196
r_nbd_refined	0.188
r_xyhbond_nbd_refined	0.178
r_nbd_other	0.167
r_symmetry_nbd_other	0.162
r_nbtor_refined	0.158
r_symmetry_metal_ion_refined	0.13
r_metal_ion_refined	0.126
r_symmetry_nbtor_other	0.072
r_symmetry_xyhbond_nbd_refined	0.061
r_chiral_restr	0.05
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	2589
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	71

Software

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