4MCI | pdb_00004mci

Crystal structure of uridine phosphorylase from vibrio fischeri es114 complexed with DMSO, NYSGRC Target 029520.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4LNH	PDB ENTRY 4LNH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.2 M AMMONIUM SULFATE, 0.1 M HEPES:NAOH, PH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.993	α = 90
b = 163.993	β = 90
c = 58.9	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		2013-08-13		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	2.01	81.996	98.2	0.088	12.2	6.7	19810	19810

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	2.01	2.12	89.4		0.482	0.482	1.6	4.1	2594

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 4LNH	2.01	47.34	19760	1008	97.97	0.1789	0.1778	0.18	0.1986	0.2	RANDOM	34.5363

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]
-4.62			-4.62		9.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.524
r_dihedral_angle_4_deg	18.786
r_dihedral_angle_3_deg	12.3
r_dihedral_angle_1_deg	6.03
r_mcangle_it	2.413
r_scbond_it	2.393
r_mcbond_it	1.452
r_angle_refined_deg	1.219
r_chiral_restr	0.079
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.524
r_dihedral_angle_4_deg	18.786
r_dihedral_angle_3_deg	12.3
r_dihedral_angle_1_deg	6.03
r_mcangle_it	2.413
r_scbond_it	2.393
r_mcbond_it	1.452
r_angle_refined_deg	1.219
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1886
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	57

Software

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

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.