9INR | pdb_00009inr

Crystal structure of PIN1 in complex with inhibitor C3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.1 M MES (pH 6.5), 0.2 M Ammonium sulfate, 24~33% (v/v) PEG5K MME

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.59	α = 90
b = 176.64	β = 90
c = 42.63	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	PIXEL	DECTRIS PILATUS 6M		2022-12-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.979183	SSRF	BL18U1

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	1.93	34.554	100	0.188	0.992	8.1	12.4		32019

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.98			0.671

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.93	34.554	31962	1578	99.969	0.195	0.1929	0.2295	39.597

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]
1.811			-1.498		-0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.591
r_dihedral_angle_4_deg	16.03
r_dihedral_angle_3_deg	14.359
r_dihedral_angle_1_deg	7.296
r_lrange_it	7.242
r_lrange_other	7.192
r_scangle_it	6.068
r_scangle_other	6.037
r_scbond_it	4.266
r_scbond_other	4.247
r_mcangle_it	4.073
r_mcangle_other	4.072
r_mcbond_it	3.136
r_mcbond_other	3.132
r_angle_refined_deg	1.78
r_angle_other_deg	1.394
r_nbd_other	0.224
r_symmetry_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.21
r_nbd_refined	0.204
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.146
r_symmetry_xyhbond_nbd_other	0.126
r_chiral_restr	0.122
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_xyhbond_nbd_other	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2288
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing