3TDB | pdb_00003tdb

Human Pin1 bound to trans peptidomimetic inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	1.9-2.2 M ammonium sulfate, 1% PEG400 at pH 7.5 in 50 mM HEPES buffer, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.273	α = 90
b = 69.273	β = 90
c = 79.657	γ = 120

Symmetry
Space Group	P 31 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	IMAGE PLATE	MACSCIENCE DIP100		2004-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	MACSCIENCE	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.26	50	97.5			10488	10226	-3	-3

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	2.26	2.34	85.9		0.301	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.267	47.95	10472	10205	1037	97.45	0.2212	0.2168	0.2127	0.2561	0.2505	RANDOM	29.9775

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]
0.8	0.4		0.8		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.54
r_dihedral_angle_4_deg	17.339
r_dihedral_angle_3_deg	15.647
r_dihedral_angle_1_deg	6.274
r_scangle_it	2.865
r_scbond_it	1.859
r_angle_refined_deg	1.516
r_mcangle_it	1.296
r_mcbond_it	0.777
r_nbtor_refined	0.293
r_symmetry_hbond_refined	0.205
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.162
r_symmetry_vdw_refined	0.139
r_chiral_restr	0.097
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1164
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	63

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction