5VTK | pdb_00005vtk

Structure of Pin1 WW Domain Variant 1 with beta3-Ser Loop Substitution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VTJ	PDB entry 5VTJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.1 M HEPES, pH 7.5, 4.3 M sodium chloride (Hampton CSII #36), crystal grew after ~6 months, treated with 4:1 (CS2 #36):glycerol prior to freezing in cryostream

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.629	α = 90
b = 47.629	β = 90
c = 60.741	γ = 120

Symmetry
Space Group	P 65 2 2

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	APEX II CCD		2014-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER IMUS MICROFOCUS	0.72

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	1.99	34.12	99.7	0.102	38.41	40.8		3112			10.2

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	1.99	2.02	97.7		0.324	11.27	24.6

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 (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 5VTJ	1.99	34.12	2804	287	99.87	0.1625	0.15685	0.17	0.22098	0.22	RANDOM	14.392

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]
-0.03	-0.01		-0.03		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.732
r_dihedral_angle_3_deg	12.501
r_long_range_B_refined	7.025
r_dihedral_angle_1_deg	6.794
r_long_range_B_other	6.542
r_dihedral_angle_4_deg	6.347
r_scangle_other	3.619
r_mcangle_it	3.469
r_mcangle_other	3.461
r_scbond_it	2.158
r_mcbond_other	2.091
r_mcbond_it	2.083
r_scbond_other	2.017
r_angle_refined_deg	1.86
r_angle_other_deg	1.134
r_chiral_restr	0.124
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	281
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XPREP	data reduction
APEX 2	data collection
PHASER	phasing
XPREP	data scaling