1TP3 | pdb_00001tp3

PDZ3 domain of PSD-95 protein complexed with KKETPV peptide ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BE9	PDB ENTRY 1BE9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	295	1.0 M sodium citrate, 0.1 M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.4	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.663	α = 90
b = 89.663	β = 90
c = 89.663	γ = 90

Symmetry
Space Group	P 41 3 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	MARRESEARCH		2004-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.99	23.96	99.7	6	11.58	8916	8916	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.06	99.1

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BE9	1.99	19.57	1	8486	8486	423	99.72	0.2328	0.22788	0.2247	0.23	0.2961	RANDOM	25.567

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	9.029
r_scangle_it	6.682
r_scbond_it	4.129
r_angle_refined_deg	2.721
r_mcangle_it	2.599
r_mcbond_it	1.618
r_angle_other_deg	1.223
r_symmetry_vdw_refined	0.398
r_symmetry_vdw_other	0.358
r_nbd_other	0.28
r_symmetry_hbond_refined	0.251
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.175
r_nbtor_other	0.107
r_bond_refined_d	0.038
r_gen_planes_refined	0.013
r_gen_planes_other	0.008
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	908
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
d*TREK	data scaling
XTALVIEW	refinement