5DTH | pdb_00005dth

Crystal structure of MUPP1 PDZ8 domain from rattus norvegicus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DAZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	0.2 M NaI, 25% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.104	α = 90
b = 39.242	β = 92.73
c = 134.449	γ = 90

Symmetry
Space Group	C 1 2 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 315r		2014-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9792	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	50	98.4	0.107	0.13	0.074	8.2	2.9		31967

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	99.5		0.663	0.816	0.469	0.58		2.9	1543

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	FREE R-VALUE	2DAZ	1.95	40.64	30350	1614	85.65	0.2266	0.2247	0.2392	0.2648	0.2825	RANDOM	24.19

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]
10.51		0.39	-3.47		-7.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.865
r_dihedral_angle_4_deg	15.071
r_dihedral_angle_3_deg	14.607
r_dihedral_angle_1_deg	6.697
r_mcangle_it	3.424
r_mcbond_it	2.476
r_mcbond_other	2.476
r_angle_other_deg	2.213
r_angle_refined_deg	2.041
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_bond_other_d	0.013
r_gen_planes_refined	0.013
r_gen_planes_other	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3181
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data reduction