6SPV | pdb_00006spv

Crystal structure of PDZ1-2 from PSD-95

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RL7	3rl7, 3rl8
experimental model	PDB	3RL8	3rl7, 3rl8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.2 M calcium acetate; 0.1 M sodium cacodylate; 40% v/v PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.38	α = 90
b = 50.38	β = 90
c = 178.27	γ = 90

Symmetry
Space Group	I 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 2M		2014-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.920	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.04	48.48	99.4	0.05	0.999	24.4	11.1		14015

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.04	2.09	97.6		0.547	0.851	2.8	5.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3rl7, 3rl8	2.04	48.48	13994	735	99.389	0.226	0.2244	0.23	0.2597	0.26	65.303

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]
-0.256			-0.256		0.513

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.327
r_dihedral_angle_3_deg	11.507
r_dihedral_angle_4_deg	9.216
r_lrange_it	7.107
r_dihedral_angle_1_deg	5.223
r_scangle_it	2.889
r_mcangle_it	2.565
r_scbond_it	1.752
r_mcbond_it	1.436
r_angle_refined_deg	0.996
r_nbtor_refined	0.294
r_nbd_refined	0.179
r_symmetry_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.132
r_xyhbond_nbd_refined	0.1
r_chiral_restr	0.064
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1416
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
SCALA	data scaling
pointless	data scaling
PHASER	phasing