2GZV | pdb_00002gzv

The cystal structure of the PDZ domain of human PICK1

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.2 M Ammonium-acetate, 0.1 M Bis-Tris, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.588	α = 90
b = 37.257	β = 95.75
c = 29.442	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	MARRESEARCH	mirrors	2006-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97925	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.12	29.3	98.4	0.0565			33346	32802

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.12	1.22	94.8		0.0126	7.97	3.04	7289

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 ENTRY 2FNE	1.12	29.3	33346	31143	1659	98.49	0.15007	0.15007	0.14911	0.16	0.16865	0.17	RANDOM	9.872

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]
-0.15		-0.11	-0.03		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.729
r_dihedral_angle_4_deg	23.812
r_dihedral_angle_3_deg	9.157
r_sphericity_free	6.72
r_dihedral_angle_1_deg	6.217
r_scangle_it	5.449
r_sphericity_bonded	4.632
r_scbond_it	4.356
r_mcangle_it	3.608
r_mcbond_it	3.019
r_rigid_bond_restr	2.702
r_mcbond_other	2.445
r_angle_refined_deg	1.332
r_angle_other_deg	0.878
r_symmetry_vdw_other	0.238
r_nbd_refined	0.211
r_nbd_other	0.174
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.163
r_symmetry_vdw_refined	0.111
r_nbtor_other	0.092
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
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	144
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data scaling
PHASER	phasing