7YAN | pdb_00007yan

UDP-glucuronosyltransferase2B17 C-terminal domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	20% PEG 6000, 0.2M Na-Tartrate, 0.2M KCl, 2% glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.15	α = 99.245
b = 57.308	β = 94.715
c = 74.074	γ = 90.118

Symmetry
Space Group	P 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 PILATUS 200K		2021-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.5	19.11	97.45	0.0978	0.985	8.05	2.7		20837

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.589			0.893

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6IPB	2.5	19.11	20837	1012	97.469	0.271	0.2677	0.27	0.3308	0.33	18.094

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]
0.008	0.001	0.025	0.002	-0.027	-0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.607
r_dihedral_angle_3_deg	17.184
r_dihedral_angle_4_deg	15.802
r_dihedral_angle_1_deg	7.858
r_lrange_other	4.689
r_lrange_it	4.688
r_mcangle_it	2.153
r_mcangle_other	2.153
r_scangle_it	1.917
r_scangle_other	1.917
r_angle_refined_deg	1.459
r_mcbond_it	1.225
r_mcbond_other	1.224
r_angle_other_deg	1.138
r_scbond_it	1.108
r_scbond_other	1.108
r_symmetry_xyhbond_nbd_refined	0.414
r_nbd_other	0.336
r_symmetry_nbd_refined	0.304
r_nbd_refined	0.211
r_symmetry_nbd_other	0.198
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.156
r_symmetry_xyhbond_nbd_other	0.143
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.051
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5052
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
SCALA	data scaling
MOLREP	phasing