4LDN | pdb_00004ldn

Crystal structure of a putative purine nucleoside phosphorylase from Vibrio fischeri ES114 (Target NYSGRC-029521)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	298	Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT), Reservoir (MCSG2 #05 - 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4), Cryoprotection (33% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.115	α = 90
b = 163.115	β = 90
c = 45.339	γ = 120

Symmetry
Space Group	H 3 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	CCD	RAYONIX MX225HE	MIRRORS	2013-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.979310	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.48	40	99.7	0.112	23.7	14.8		37977			12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.48	1.51	96.8		0.801	3.7	13.5	1837

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.48	30.84	37970	1896	99.67	0.1636	0.1624	0.1614	0.187	0.1866	RANDOM	18.3874

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]
-0.62	-0.62		-0.62		2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.118
r_dihedral_angle_4_deg	18.066
r_dihedral_angle_3_deg	12.397
r_dihedral_angle_1_deg	6.004
r_mcangle_it	2.119
r_angle_refined_deg	1.636
r_mcbond_it	1.251
r_mcbond_other	1.248
r_angle_other_deg	0.768
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.118
r_dihedral_angle_4_deg	18.066
r_dihedral_angle_3_deg	12.397
r_dihedral_angle_1_deg	6.004
r_mcangle_it	2.119
r_angle_refined_deg	1.636
r_mcbond_it	1.251
r_mcbond_other	1.248
r_angle_other_deg	0.768
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1901
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
Aimless	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

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.