6QMM | pdb_00006qmm

Crystal structure of Synecochoccus Spermidine Synthase in complex with putrescine, spermidine and MTA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YUV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294.15	0.1 M MES pH 6.0, 45 % v/v Pentaerythritol propoxylate (5/4 PO/OH)

Crystal Properties
Matthews coefficient	Solvent content
2.16	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.64	α = 90
b = 63.82	β = 92.72
c = 73.5	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	PIXEL	DECTRIS EIGER X 4M		2016-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.18	48.17	99	0.0721	0.083	0.997	16.18	4.2		27391

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.27			0.226	0.261	0.956

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	4YUV	2.18	48.17	26118	1375	98.3	0.1441	0.1416	0.15	0.1911	0.2	RANDOM	17.36

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]
1.21		0.43	-0.07		-1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.971
r_dihedral_angle_4_deg	22.329
r_dihedral_angle_3_deg	14.88
r_dihedral_angle_1_deg	7.423
r_angle_other_deg	2.618
r_angle_refined_deg	2.489
r_mcangle_it	2.093
r_mcbond_other	1.263
r_mcbond_it	1.262
r_chiral_restr	0.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.971
r_dihedral_angle_4_deg	22.329
r_dihedral_angle_3_deg	14.88
r_dihedral_angle_1_deg	7.423
r_angle_other_deg	2.618
r_angle_refined_deg	2.489
r_mcangle_it	2.093
r_mcbond_other	1.263
r_mcbond_it	1.262
r_chiral_restr	0.127
r_bond_other_d	0.035
r_gen_planes_other	0.032
r_bond_refined_d	0.023
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4411
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	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.