9PDZ | pdb_00009pdz

Crystal structure of a Spermidine binding protein isolated from Synechococcus CC9311

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	20% (w/v) PEG 8000, 100 mM HEPES/ Sodium hydroxide pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.08	α = 90
b = 65.98	β = 98.633
c = 64.37	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	80	PIXEL	DECTRIS PILATUS 12M		2020-06-26	M	SINGLE WAVELENGTH
2	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2020-06-26	M	SINGLE WAVELENGTH
3	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2020-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	2.7552	Diamond	I23
2	SYNCHROTRON	DIAMOND BEAMLINE I23	4.2753	Diamond	I23
3	SYNCHROTRON	DIAMOND BEAMLINE I23	4.5082	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.796	45.847	90.3	0.999	19.6	11.4		27220

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83			0.611

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	FREE R-VALUE	1.8	45.847	27216	1322	90.455	0.185	0.1831	0.1835	0.2194	0.2198	37.303

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]
-1.131		0.428	0.879		0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.603
r_dihedral_angle_6_deg	15.13
r_dihedral_angle_3_deg	14.45
r_lrange_it	9.239
r_lrange_other	9.198
r_dihedral_angle_1_deg	6.804
r_scangle_it	6.44
r_scangle_other	6.439
r_scbond_it	4.639
r_scbond_other	4.637
r_mcangle_it	4.204
r_mcangle_other	4.202
r_mcbond_it	3.075
r_mcbond_other	3.073
r_angle_refined_deg	2.343
r_angle_other_deg	0.892
r_symmetry_nbd_refined	0.37
r_symmetry_xyhbond_nbd_refined	0.263
r_nbd_refined	0.225
r_symmetry_xyhbond_nbd_other	0.206
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.169
r_symmetry_nbd_other	0.167
r_chiral_restr	0.123
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2262
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CRANK2	phasing