1NTE | pdb_00001nte

CRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OF SYNTENIN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N99	PDB ENTRY 1N99

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294	PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.41	12.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.292	α = 90
b = 42.57	β = 108.71
c = 31.038	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	ADSC QUANTUM 4		2002-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	0.97946	NSLS	X9B

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	1.1	12.16	73.3	0.042	28.5	3.1	18559	18559	1	-3	7.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 1N99	1.24	12.16	1	16535	15684	851	93.13	0.11533	0.11325	0.12	0.15331	0.16	RANDOM	10.391

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]
0.04		0.26	-0.18		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.398
r_sphericity_free	5.089
r_scangle_it	3.372
r_sphericity_bonded	3.222
r_scbond_it	2.474
r_mcangle_it	1.956
r_angle_other_deg	1.885
r_angle_refined_deg	1.626
r_mcbond_it	1.312
r_rigid_bond_restr	1.271
r_symmetry_vdw_other	0.332
r_xyhbond_nbd_refined	0.254
r_nbd_other	0.252
r_nbd_refined	0.246
r_symmetry_hbond_refined	0.184
r_chiral_restr	0.115
r_symmetry_vdw_refined	0.103
r_nbtor_other	0.085
r_gen_planes_other	0.019
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	608
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing