1ZX6

High-resolution crystal structure of yeast Pin3 SH3 domain

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OOT	PDB Entry: 1oot

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.04	α = 90
b = 27.36	β = 102.87
c = 24	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		2005-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.813	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	20	94.2	0.069	7.9	2	7155	7155	-3	-3	21

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.7	96.8		0.312	2.6	1.9	1187

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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: 1oot	1.6	20	-3	7155	7155	358	94.31	0.18347	0.18347	0.18157	0.19	0.22089	0.24	RANDOM	21.942

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]
-0.82		0.36	2.73		-1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	27.413
r_dihedral_angle_2_deg	26.177
r_dihedral_angle_3_deg	10.245
r_dihedral_angle_1_deg	5.335
r_scangle_it	3.03
r_scbond_it	2.536
r_mcangle_it	1.605
r_angle_refined_deg	1.451
r_mcbond_it	1.437
r_angle_other_deg	0.78
r_symmetry_vdw_refined	0.379
r_mcbond_other	0.338
r_nbd_refined	0.191
r_nbtor_refined	0.186
r_symmetry_hbond_refined	0.174
r_nbd_other	0.173
r_symmetry_vdw_other	0.164
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.096
r_nbtor_other	0.085
r_bond_refined_d	0.013
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	448
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing