8CVC | pdb_00008cvc

Structure of 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
2.18	43.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.911	α = 90
b = 79.761	β = 111.054
c = 56.187	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	MARMOSAIC 300 mm CCD		2020-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.79	50	100	0.067	0.026	0.889	24.4	7.5		34735

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	1.79	1.82	100		0.456	0.199	0.889	3.8	6.3

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	1.791	40.654	34735	1839	99.716	0.174	0.1729	0.1831	0.1943	0.2023	20.243

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]
-0.002		-0.001	0.002		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.751
r_dihedral_angle_4_deg	12.377
r_dihedral_angle_3_deg	12.009
r_dihedral_angle_1_deg	6.513
r_lrange_it	3.951
r_lrange_other	3.875
r_scangle_it	2.102
r_scangle_other	2.102
r_mcangle_it	1.864
r_mcangle_other	1.864
r_scbond_it	1.261
r_scbond_other	1.261
r_angle_refined_deg	1.2
r_angle_other_deg	1.186
r_mcbond_it	1.069
r_mcbond_other	1.068
r_nbd_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.168
r_symmetry_nbd_other	0.164
r_nbtor_refined	0.157
r_symmetry_nbd_refined	0.138
r_xyhbond_nbd_refined	0.13
r_nbd_other	0.121
r_metal_ion_refined	0.082
r_symmetry_nbtor_other	0.073
r_symmetry_metal_ion_refined	0.071
r_chiral_restr	0.057
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	2595
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	70

Software

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