2QG1 | pdb_00002qg1

Crystal structure of the 11th PDZ domain of MPDZ (MUPP1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HE2	PDB entries 2HE2, 1TP3
experimental model	PDB	1TP3	PDB entries 2HE2, 1TP3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	0.8M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.409	α = 90
b = 36.919	β = 90
c = 63.609	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD		2007-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9182	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.4	31.8	96.6	0.073	0.073	13.5	4.6	15501	15501

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.4	1.48	94.7		0.394	0.394	2.6	3.8	8319

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 2HE2, 1TP3	1.4	31.8	14686	14686	780	96.16	0.17252	0.17252	0.16937	0.18	0.23418	0.25	RANDOM	14.93

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]
0.72			-1.84		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.514
r_dihedral_angle_4_deg	15.867
r_sphericity_free	12.968
r_dihedral_angle_3_deg	12.69
r_scangle_it	9.261
r_scbond_it	7.792
r_sphericity_bonded	6.723
r_mcangle_it	6.359
r_dihedral_angle_1_deg	5.724
r_mcbond_it	5.557
r_rigid_bond_restr	4.205
r_mcbond_other	3.847
r_angle_refined_deg	1.489
r_angle_other_deg	0.865
r_symmetry_vdw_refined	0.259
r_symmetry_vdw_other	0.23
r_symmetry_hbond_refined	0.222
r_nbd_refined	0.208
r_nbd_other	0.194
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.162
r_nbtor_other	0.09
r_chiral_restr	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	667
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing