9GN8 | pdb_00009gn8

Crystal Structure of UFC1 E149D

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z6O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	2% (v/v) Tacsimate Ph 7.0, 0.1M Hepes pH 7.5, 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.398	α = 90
b = 46.829	β = 90
c = 80.201	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS PILATUS 200K		2022-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.397	40.47	99.98	0.0388	1	14.18	2		33844			18.535

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	100		1.428	0.398	0.63	2

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.96	38.873	11809	610	94.253	0.198	0.1946	0.1961	0.2573	0.2632	20.328

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]
0.942			-0.368		-0.573

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.161
r_dihedral_angle_3_deg	15.218
r_dihedral_angle_4_deg	14.95
r_dihedral_angle_1_deg	6.585
r_lrange_it	5.589
r_lrange_other	5.415
r_scangle_other	3.084
r_scangle_it	3.083
r_mcangle_it	2.789
r_mcangle_other	2.787
r_scbond_it	1.889
r_scbond_other	1.871
r_mcbond_it	1.708
r_mcbond_other	1.707
r_angle_other_deg	1.314
r_angle_refined_deg	1.271
r_nbd_other	0.213
r_symmetry_nbd_other	0.195
r_nbd_refined	0.182
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbd_refined	0.095
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.082
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1384
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building