3E56 | pdb_00003e56

The 2.0 Angstrom Resolution Crystal Structure of NpR1517, a Putative Heterocyst Differentiation Inhibitor from Nostoc punctiforme

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	.02M HEPES, 20% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.74	29.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.336	α = 90
b = 56.336	β = 90
c = 56.491	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	BRUKER SMART 6000	mirrors	2008-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	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	2.01	39.9	95.9	0.06	76.22	105.86	6345	6345		3	24.37

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	2.01	2.05	95.9		0.28	9.15	19.53	1604

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	sulfur anomalous scattering	THROUGHOUT	2.01	39.9	3	6053	291	98.59	0.19007	0.18795	0.19	0.23683	0.24	RANDOM	24.854

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]
0.31			0.31		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.2
r_dihedral_angle_4_deg	19.471
r_dihedral_angle_3_deg	16.702
r_dihedral_angle_1_deg	6.272
r_sphericity_free	6.058
r_scangle_it	5.541
r_scbond_it	4.644
r_rigid_bond_restr	4.537
r_sphericity_bonded	3.061
r_mcangle_it	2.165
r_angle_refined_deg	1.596
r_mcbond_it	1.351
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.23
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.183
r_symmetry_hbond_refined	0.125
r_chiral_restr	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	611
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM2	data collection
SAINT	data reduction
SADABS	data scaling
SHELXS	phasing