3HPC | pdb_00003hpc

Crystal structure of SNX5-PX domain in P21 space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	277	The protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml and crystallization were obtained using an optimized crystallization condition of 8ul of protein vs 1ul of reservoir solution (0.2M NH4CH3COO, 0.1M Sodium cacodylate tryhydrate pH 6.5, 30% PEG 4000), VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.300956	46.543972

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.598	α = 90
b = 41.424	β = 92.98
c = 47.227	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	CCD	RIGAKU SATURN 944	MIRRORS	2007-06-15	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.47	31.12	98.3	0.043	20.1	4.13		28322		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.47	1.52	90.8		0.325	1.4	2.65

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	3HPB	1.47	31.12	26873	1440	98.2	0.187	0.184	0.18	0.234	0.23	RANDOM	26.45

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]
-0.1		-0.01	0.61		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.13
r_sphericity_free	14.952
r_dihedral_angle_4_deg	14.311
r_dihedral_angle_3_deg	12.856
r_sphericity_bonded	11.584
r_scangle_it	8.036
r_dihedral_angle_1_deg	5.739
r_scbond_it	5.567
r_mcangle_it	4.047
r_rigid_bond_restr	3.334
r_mcbond_it	2.827
r_angle_refined_deg	1.296
r_chiral_restr	0.097
r_gen_planes_refined	0.015
r_bond_refined_d	0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1323
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	1

Software

Software
Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling