9I9P | pdb_00009i9p

Crystal Structure of UFC1 W145H

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	298	0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.548	α = 90
b = 46.512	β = 97.742
c = 45.588	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER X 9M		2024-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

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	2.022	32.405	98.8	0.414	0.925	2.6	3.5		9919			15.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.022	5.479	100		1.223	0.754	0.378	1.2	3.5

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	2.022	32.405	9884	487	98.476	0.238	0.2362	0.2414	0.2672	0.272	17.466

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]
-0.592		-0.245	-0.897		1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.344
r_dihedral_angle_4_deg	22.045
r_dihedral_angle_3_deg	16.202
r_dihedral_angle_1_deg	6.562
r_lrange_it	4.27
r_lrange_other	4.171
r_mcangle_it	1.461
r_mcangle_other	1.46
r_angle_refined_deg	1.439
r_angle_other_deg	1.282
r_scangle_other	1.261
r_scangle_it	1.26
r_mcbond_it	0.877
r_mcbond_other	0.875
r_scbond_it	0.763
r_scbond_other	0.762
r_symmetry_nbd_refined	0.42
r_nbd_other	0.322
r_symmetry_nbd_other	0.213
r_nbd_refined	0.196
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.148
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1269
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
autoPROC	data scaling
Coot	model building