7AVC | pdb_00007avc

DoBi scaffold based on PIH1D1 N-terminal domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PSF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	10% glycerol, 4M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.723	α = 90
b = 72.723	β = 90
c = 192.775	γ = 120

Symmetry
Space Group	H 3 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	PIXEL	DECTRIS PILATUS 6M		2016-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.2	38.27	97.1	0.247	0.261	0.083	0.978	5.4	9.6		59704			11.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	74.4		1.215	1.32	0.5	0.498	1.3	6.4

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4PSF	1.2	38.27	59703	3028	96.869	0.173	0.13984	0.13611	0.17	0.15419	0.18	19.703

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]
0.148	0.074		0.148		-0.479

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.651
r_dihedral_angle_4_deg	25.033
r_dihedral_angle_3_deg	13.32
r_lrange_it	6.827
r_lrange_other	6.5
r_dihedral_angle_1_deg	6.092
r_scangle_it	5.4
r_scangle_other	5.397
r_scbond_it	3.915
r_scbond_other	3.912
r_mcangle_it	3.514
r_mcangle_other	3.512
r_mcbond_it	2.352
r_mcbond_other	2.339
r_angle_other_deg	2.335
r_angle_refined_deg	1.921
r_symmetry_nbd_refined	0.249
r_nbd_other	0.243
r_nbd_refined	0.231
r_symmetry_xyhbond_nbd_refined	0.217
r_symmetry_nbd_other	0.21
r_xyhbond_nbd_refined	0.209
r_nbtor_refined	0.182
r_symmetry_metal_ion_refined	0.146
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.083
r_metal_ion_refined	0.08
r_bond_other_d	0.034
r_gen_planes_other	0.031
r_bond_refined_d	0.017
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1132
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing