9GLH | pdb_00009glh

Crystal Structure of UFC1 T106S

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	6	293	1.4M Sodium Malonate dibasic monohydrate pH 6.0.

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.16	α = 90
b = 47.16	β = 90
c = 143.616	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 EIGER X 16M		2022-11-09	M	SINGLE WAVELENGTH

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

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	1.115	33.35	98.88	0.02378	1	14.67	2		63633			12.88

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	1.115	1.154	92.21		0.3585	0.818	2.5	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	1.115	33.35	63633	3175	98.887	0.175	0.174	0.174	0.192	0.192	14.251

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]
-0.114			-0.114		0.228

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.69
r_dihedral_angle_4_deg	12.296
r_dihedral_angle_3_deg	10.393
r_dihedral_angle_1_deg	6.359
r_lrange_it	4.429
r_lrange_other	4.246
r_scangle_it	3.523
r_scangle_other	3.517
r_scbond_it	2.549
r_scbond_other	2.501
r_angle_refined_deg	2.002
r_mcangle_it	1.763
r_mcangle_other	1.762
r_angle_other_deg	1.556
r_mcbond_other	1.304
r_mcbond_it	1.303
r_symmetry_nbd_refined	0.417
r_nbd_other	0.263
r_nbd_refined	0.229
r_symmetry_xyhbond_nbd_refined	0.207
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.178
r_chiral_restr	0.128
r_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1337
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	5

Software

Software
Software Name	Purpose
autoPROC	data processing
autoPROC	data reduction
autoPROC	data scaling
REFMAC	refinement