8RIH | pdb_00008rih

Crystal structure of the Saccharomyces cerevisiae URH1p riboside hydrolase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q8F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291.15	100 mM TrisHCl, 800 mM LiCl, 32% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.284	α = 90
b = 140.284	β = 90
c = 81.343	γ = 120

Symmetry
Space Group	P 63

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	CRLs, multilayer mirrors	2022-07-22	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)	Rpim 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	2.6	121.49	94.1	0.167	0.981	5.9	12.9		13763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.89	81.8		0.988	0.57	1.8	11.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.74	121.49	13542	714	56.1	0.188	0.1859	0.2	0.2245	0.23	Random selection	39.22

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]
0.035	0.017		0.035		-0.112

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.069
r_dihedral_angle_6_deg	13.936
r_dihedral_angle_1_deg	6.789
r_lrange_it	4.743
r_lrange_other	4.743
r_dihedral_angle_2_deg	4.505
r_scangle_it	2.456
r_scangle_other	2.456
r_mcangle_it	1.97
r_mcangle_other	1.97
r_scbond_it	1.449
r_scbond_other	1.449
r_mcbond_it	1.151
r_mcbond_other	1.149
r_angle_refined_deg	0.908
r_angle_other_deg	0.295
r_nbd_refined	0.199
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.177
r_nbd_other	0.176
r_symmetry_xyhbond_nbd_other	0.175
r_xyhbond_nbd_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.14
r_symmetry_nbtor_other	0.076
r_ncsr_local_group_1	0.059
r_chiral_restr	0.041
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5220
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing