7NVJ | pdb_00007nvj

Crystal structure of UFC1 Y110A & F121A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z6P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.1M HEPES pH 7.5, 2M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.161	α = 90
b = 46.161	β = 90
c = 143.755	γ = 90

Symmetry
Space Group	P 41 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	298	PIXEL	DECTRIS PILATUS 200K		2021-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.2	33.24	99.8	0.153	0.99	13.33	1.2		8491			25.44

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	2.2	2.279	99.14		0.71	0.47	2.7	1.1

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2Z6P	2.2	33.24	8491	444	99.824	0.196	0.1928	0.2	0.246	0.25	Random selection	26.854

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]
0.088			0.088		-0.175

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.469
r_dihedral_angle_3_deg	15.763
r_dihedral_angle_4_deg	11.327
r_lrange_it	7.385
r_lrange_other	7.382
r_dihedral_angle_1_deg	6.44
r_scangle_it	4.126
r_scangle_other	4.124
r_mcangle_it	3.538
r_mcangle_other	3.536
r_scbond_it	2.648
r_scbond_other	2.646
r_mcbond_it	2.239
r_mcbond_other	2.238
r_angle_refined_deg	1.468
r_angle_other_deg	1.258
r_symmetry_nbd_refined	0.25
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.219
r_symmetry_xyhbond_nbd_refined	0.213
r_symmetry_nbd_other	0.191
r_nbd_other	0.175
r_nbtor_refined	0.169
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1316
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing