9FI9 | pdb_00009fi9

Human PIF + Z48847594 (OCCUPANCY 0.7)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HPH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	XCHEM 0.045ULS COMPOUND (0.5M) IN DMSO ECHO DISPENSED INTO CRYSTAL DROP DROP = 0.3ULS PROTEIN + 0.3ULS WELL +0.001ULS SEEDS. PROTEIN = 25ULS 30MGS/ML HUMAN PIF1 (206-620) IN 10MM TRIS PH 7.5, 175MM NACL, 2%GLYCEROL, 5MM DTT, 0.1MM PMSF + 21ULS 10MM TRIS, 2.7ULS 0.2M MGCL2, 5ULS 100MM AMPPNP + 27ULS H2O. WELL = 4% GLYCEROL, 27% PEG 2KMME, 0.1M NAACETATE, 0.1M TRIS PH8.5. SET UP ON DOUGLAS INSTRUMENTS ROBOT - TRAY ON ICE - SET-UP ROOM TEMPERATURE - CRYSTALLISED 4 DEGREES C.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.6	α = 90
b = 143.714	β = 90
c = 77.238	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2018-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.727	27.849	99.6	0.999	19.5	6.5		43220

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	1.727	1.772			0.866	2.1

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.727	27.849	43195	2134	99.617	0.156	0.1545	0.1545	0.1943	0.1943	32.497

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]
-2.317			1.102		1.214

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.332
r_dihedral_angle_3_deg	14.436
r_lrange_it	11.26
r_dihedral_angle_2_deg	8.88
r_dihedral_angle_1_deg	6.064
r_scangle_it	5.068
r_scbond_it	3.347
r_mcangle_it	3.015
r_mcbond_it	2.128
r_angle_refined_deg	1.81
r_nbtor_refined	0.306
r_metal_ion_refined	0.259
r_xyhbond_nbd_refined	0.242
r_symmetry_nbd_refined	0.231
r_nbd_refined	0.23
r_symmetry_xyhbond_nbd_refined	0.225
r_chiral_restr	0.119
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3185
Nucleic Acid Atoms
Solvent Atoms	614
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
REFMAC	phasing