3KBO | pdb_00003kbo

2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium in Complex with NADP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.3M NDSB-211, 30% PEG 3350, 0.2M Sodium acetate, 0.1M Bis-Tris pH 6.5, 10mm NADP, VAPOR DIFFUSION, HANGING DROP, temperature 295K; Cryo: oil, paratone

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 279.621	α = 90
b = 45.585	β = 101.58
c = 112.335	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 225 mm CCD	Beryllium lenses	2009-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.14	30	98.2	0.084	27	6.6	75710	75710		-3	34.7

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	2.14	2.18	93.5		0.491	3.5	6	3610

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.14	29.93	71864	71864	3806	98	0.21387	0.21387	0.21092	0.2192	0.26879	0.2754	RANDOM	27.209

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]
-1.57		0.23	5.13		-3.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.664
r_dihedral_angle_3_deg	11.693
r_dihedral_angle_4_deg	10.682
r_scangle_it	4.87
r_scbond_it	3.469
r_dihedral_angle_1_deg	2.762
r_mcangle_it	2.147
r_angle_refined_deg	1.453
r_mcbond_it	1.286
r_angle_other_deg	0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.664
r_dihedral_angle_3_deg	11.693
r_dihedral_angle_4_deg	10.682
r_scangle_it	4.87
r_scbond_it	3.469
r_dihedral_angle_1_deg	2.762
r_mcangle_it	2.147
r_angle_refined_deg	1.453
r_mcbond_it	1.286
r_angle_other_deg	0.87
r_mcbond_other	0.375
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9900
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	243

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

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.