1MJF

PUTATIVE SPERMIDINE SYNTHETASE FROM PYROCOCCUS FURIOSUS PFU-132382

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1INL	pdb entry 1INL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	291	calcium chloride, PEG400, pH 7.5, microbatch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.639	α = 90
b = 110.821	β = 90
c = 49.256	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV	confocal	2001-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-D	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	30	90.9	0.048	36			44968		-3	24

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	47.1		0.193	7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	AUTOMATED MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1INL	1.798	72.55	42629	42629	2272	90.69	0.20655	0.20655	0.20482	0.24156	RANDOM	22.253

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]
-0.55			0.79		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.156
r_scangle_it	2.025
r_scbond_it	1.188
r_angle_refined_deg	1.008
r_mcangle_it	0.845
r_angle_other_deg	0.718
r_mcbond_it	0.447
r_symmetry_vdw_other	0.313
r_nbd_other	0.221
r_nbd_refined	0.173
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.118
r_nbtor_other	0.076
r_symmetry_vdw_refined	0.066
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4326
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms

Software

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