8AAI | pdb_00008aai

Crystal structure of the PDZ tandem of syntenin in complex with fragment E5

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	100mM Sodium Acetate 200mM Ammonium acetate 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.114	α = 82.71
b = 56.13	β = 83.462
c = 102.867	γ = 77.033

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M		2017-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97625	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.76	27.63	97.29	0.1388	0.08908	5.27	5.27		15909

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.76	2.859	96.74		0.4417	0.288	2.26

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1N99	2.76	27.63	15823	782	98.006	0.277	0.2746	0.27	0.3171	0.31	50.548

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]
7.622	-1.163	-0.676	-2.241	2.756	-5.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.276
r_dihedral_angle_6_deg	11.576
r_dihedral_angle_2_deg	10.986
r_dihedral_angle_1_deg	6.24
r_lrange_it	5.777
r_lrange_other	5.744
r_mcangle_it	2.538
r_mcangle_other	2.538
r_scangle_it	2.07
r_scangle_other	2.07
r_mcbond_it	1.432
r_mcbond_other	1.432
r_scbond_it	1.142
r_scbond_other	1.141
r_angle_refined_deg	0.737
r_angle_other_deg	0.294
r_nbd_refined	0.18
r_symmetry_nbd_other	0.177
r_symmetry_nbd_refined	0.171
r_nbd_other	0.159
r_nbtor_refined	0.155
r_ncsr_local_group_4	0.131
r_xyhbond_nbd_refined	0.13
r_ncsr_local_group_5	0.123
r_ncsr_local_group_2	0.12
r_ncsr_local_group_3	0.117
r_ncsr_local_group_1	0.114
r_ncsr_local_group_6	0.11
r_symmetry_xyhbond_nbd_refined	0.104
r_symmetry_xyhbond_nbd_other	0.103
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.036
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4928
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing