9IFA | pdb_00009ifa

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with hypoxanthine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7R37

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	comprising 26% (w/v) PEG 1500 with 100 mM MMT, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.929	α = 90
b = 111.929	β = 90
c = 121.961	γ = 90

Symmetry
Space Group	P 42 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	100	PIXEL	DECTRIS EIGER X 16M		2021-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2.06	48.31	94.8	0.12	0.99	17.7	22.1		45682

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	2.06	2.12			0.61

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	2.064	48.31	45633	2151	94.594	0.167	0.165	0.1748	0.206	0.214	38.425

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]
-0.24			-0.24		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.374
r_dihedral_angle_3_deg	13.481
r_dihedral_angle_2_deg	13.465
r_lrange_it	8.101
r_lrange_other	8.1
r_scangle_it	7.004
r_scangle_other	7.003
r_dihedral_angle_1_deg	6.26
r_scbond_it	4.688
r_scbond_other	4.688
r_mcangle_it	3.632
r_mcangle_other	3.632
r_mcbond_it	2.699
r_mcbond_other	2.699
r_angle_refined_deg	1.643
r_angle_other_deg	0.546
r_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.179
r_nbd_other	0.161
r_symmetry_nbd_refined	0.141
r_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.075
r_ncsr_local_group_1	0.066
r_dihedral_angle_other_2_deg	0.014
r_bond_refined_d	0.007
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	6646
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	108

Software

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