6S5U | pdb_00006s5u

Strictosidine Synthase from Ophiorrhiza pumila in complex with N-[2-(1H-Indol-3-yl)ethyl]-3-methyl-1-butanamine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FP9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	20% PEG 6000; 0.3 M MH4Cl; 0.1M Tris-HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.747	α = 90
b = 125.747	β = 90
c = 117.081	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	DECTRIS PILATUS 6M-F		2017-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

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	39.9	99.7	0.19	0.12	0.99	6.8	5.1		133410

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	2.06			0.67	0.44	0.97	2.9

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2FP9	2.03	39.9	126761	6605	99.65	0.313	0.3119	0.32	0.3338	0.34	RANDOM	16.832

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]
-1.18	-0.59		-1.18		3.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.919
r_dihedral_angle_3_deg	14.091
r_dihedral_angle_4_deg	13.565
r_dihedral_angle_1_deg	7.622
r_angle_refined_deg	1.476
r_angle_other_deg	1.177
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.919
r_dihedral_angle_3_deg	14.091
r_dihedral_angle_4_deg	13.565
r_dihedral_angle_1_deg	7.622
r_angle_refined_deg	1.476
r_angle_other_deg	1.177
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13970
Nucleic Acid Atoms
Solvent Atoms	711
Heterogen Atoms	221

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.