2VQ5

X-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine and hydroxybenzaldehyde

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VNE	PDB ENTRY 2VNE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		AMMONIUM SULFATE 1.4-1.8 M, NACL 0.2 M, ACETATE BUFFER PH 4.0-4.5

Crystal Properties
Matthews coefficient	Solvent content
3.2	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.474	α = 90
b = 86.474	β = 90
c = 117.977	γ = 120

Symmetry
Space Group	P 31 2 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	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	50	97.8	0.08	13	3.3		30118

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	98.3		0.51	2	3.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2VNE	2.09	50	28573	1508	97.67	0.22312	0.22086	0.26605	RANDOM	37.381

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]
-0.01	-0.01		-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.639
r_dihedral_angle_4_deg	19.218
r_dihedral_angle_3_deg	16.793
r_dihedral_angle_1_deg	10.238
r_scangle_it	2.754
r_scbond_it	1.84
r_mcangle_it	1.304
r_angle_refined_deg	1.288
r_mcbond_it	0.816
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.238
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2556
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing