2Q9V | pdb_00002q9v

Crystal structure of the C890S mutant of the 4th PDZ domain of human membrane associated guanylate kinase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I04	PDB entries 2I04,2PNT,2OPG
experimental model	PDB	2PNT	PDB entries 2I04,2PNT,2OPG
experimental model	PDB	2OPG	PDB entries 2I04,2PNT,2OPG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	1:2 Protein:Well solution ratio, 20% PEG 3350, 10% Ethylene glycol, 200 mM Sodium acetate, 100 mM BTP pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2	38.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.821	α = 90
b = 44.085	β = 90
c = 54.512	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	IMAGE PLATE	RIGAKU RAXIS HTC	OSMIC	2007-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2	23	96.9	0.069	0.075	27.8	7	5689	5434		2

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	2	2.11	95.1		0.29	0.313	5.7	7.2	759

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 (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 2I04,2PNT,2OPG	2	20.97	5434	5230	252	96.24	0.17021	0.16722	0.1802	0.23313	0.2342	RANDOM	23.589

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]
-0.01			-0.67		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.93
r_dihedral_angle_4_deg	12.89
r_dihedral_angle_3_deg	11.276
r_dihedral_angle_1_deg	5.684
r_scangle_it	4.95
r_scbond_it	3.267
r_mcangle_it	1.862
r_mcbond_it	1.23
r_angle_refined_deg	0.955
r_angle_other_deg	0.831
r_mcbond_other	0.266
r_symmetry_vdw_other	0.254
r_nbd_refined	0.181
r_nbd_other	0.17
r_nbtor_refined	0.16
r_symmetry_vdw_refined	0.099
r_xyhbond_nbd_refined	0.084
r_nbtor_other	0.075
r_chiral_restr	0.06
r_symmetry_hbond_refined	0.06
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	688
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms

Software

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