2F7F | pdb_00002f7f

Crystal structure of Enterococcus faecalis putative nicotinate phosphoribosyltransferase, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	100 mM HEPES, 2 M AMMONIUM SULFATE, 10% GLYCEROL, PH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.47	49.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.325	α = 90
b = 110.627	β = 90
c = 154.189	γ = 90

Symmetry
Space Group	I 2 2 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	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2005-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	50	99.8	0.101	0.066	7.3	7	41720	41577			14.6

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	2.07	99.2		0.63	0.66	2.2	6.4	4095

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1YTD	2	20	41264	40207	1308	99.91	0.2213	0.17203	0.17066	0.18	0.21362	0.17	RANDOM	27.365

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]
0.07			1.63		-1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.703
r_dihedral_angle_4_deg	24.085
r_dihedral_angle_3_deg	14.936
r_dihedral_angle_1_deg	8.12
r_scangle_it	1.868
r_mcangle_it	1.763
r_angle_refined_deg	1.365
r_scbond_it	1.207
r_mcbond_it	1.164
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.703
r_dihedral_angle_4_deg	24.085
r_dihedral_angle_3_deg	14.936
r_dihedral_angle_1_deg	8.12
r_scangle_it	1.868
r_mcangle_it	1.763
r_angle_refined_deg	1.365
r_scbond_it	1.207
r_mcbond_it	1.164
r_nbtor_refined	0.309
r_chiral_restr	0.226
r_symmetry_hbond_refined	0.223
r_xyhbond_nbd_refined	0.202
r_nbd_refined	0.185
r_symmetry_vdw_refined	0.158
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3884
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	73

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement

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.