2VSV

Crystal structure of the PDZ domain of human rhophilin-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F5Y	PDB ENTRIES 2F5Y,2OCS,2V90
experimental model	PDB	2OCS	PDB ENTRIES 2F5Y,2OCS,2V90
experimental model	PDB	2V90	PDB ENTRIES 2F5Y,2OCS,2V90

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.2M SODIUM ACETATE, 20% PEG3350; 10% ETHYLENE GLYCOL, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.1	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.25	α = 90
b = 39.89	β = 115.78
c = 73.48	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		2008-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		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	1.82	38.9	99.1	0.1	8.8	3.4		18177			10.28

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	1.82	1.92	98.5		0.33	3.2	3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 2F5Y,2OCS,2V90	1.82	66.23	17238	939	98.8	0.222	0.22	0.267	RANDOM	12.21

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]
2.36		0.72	-0.39		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.622
r_dihedral_angle_4_deg	18.991
r_dihedral_angle_3_deg	12.525
r_scangle_it	9.236
r_scbond_it	6.724
r_dihedral_angle_1_deg	6.118
r_mcangle_it	4.101
r_mcbond_it	2.811
r_angle_refined_deg	1.376
r_angle_other_deg	0.902
r_nbd_refined	0.217
r_symmetry_vdw_other	0.202
r_nbd_other	0.19
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.129
r_symmetry_vdw_refined	0.126
r_nbtor_other	0.087
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1538
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing