5DCU | pdb_00005dcu

Iridoid synthase from Catharanthus roseus - ternary complex with NADP+ and triethylene glycol carboxylic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V6G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.03	α = 90
b = 96.11	β = 90
c = 172.63	γ = 90

Symmetry
Space Group	C 2 2 21

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 PILATUS 6M		2014-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9000	Diamond	I04

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	1.4	86.32	100	0.069	0.025	0.999	16.1	8.3		149766			11.4

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	1.4	1.44	99.9		1.447	0.532	0.569	1.5	8.3	10987

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 (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2V6G	1.4	86.32	142552	7213	99.97	0.1561	0.1549	0.1795	0.1852	RANDOM	19.9

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]
0.02			0.38		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.494
r_dihedral_angle_4_deg	20.934
r_dihedral_angle_3_deg	10.47
r_dihedral_angle_1_deg	6.136
r_angle_refined_deg	1.555
r_angle_other_deg	1.16
r_mcangle_it	0.973
r_mcbond_it	0.597
r_mcbond_other	0.596
r_chiral_restr	0.098
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5765
Nucleic Acid Atoms
Solvent Atoms	869
Heterogen Atoms	134

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction