4LYY | pdb_00004lyy

Crystal structure of hypoxanthine phosphoribosyltransferase from Shewanella pealeana ATCC 700345, NYSGRC Target 029677.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J7J	PDB ENTRY 1J7J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	0.2 M sodium chloride, 0.1 M Bis-Tris:HCl, pH 5.5, 25% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.514	α = 90
b = 101.173	β = 107.38
c = 73.844	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	RAYONIX MX225HE		2013-07-18		SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9791	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.86	101.173	98.7	0.094	13.5	7.5	59642	59642

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.96	98.5		0.525	0.525	1.3	7.7	8665

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 (Observed)	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	PDB ENTRY 1J7J	1.86	70.47	59581	3017	98.56	0.1808	0.1789	0.19	0.2165	0.23	RANDOM	31.1711

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]
11.1		-16.04	-5.98		-5.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.284
r_dihedral_angle_3_deg	14.131
r_dihedral_angle_4_deg	13.336
r_dihedral_angle_1_deg	5.797
r_scbond_it	3.204
r_mcangle_it	2.849
r_mcbond_it	1.71
r_angle_refined_deg	1.458
r_chiral_restr	0.089
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.284
r_dihedral_angle_3_deg	14.131
r_dihedral_angle_4_deg	13.336
r_dihedral_angle_1_deg	5.797
r_scbond_it	3.204
r_mcangle_it	2.849
r_mcbond_it	1.71
r_angle_refined_deg	1.458
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5302
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.