3RQH

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis in complex with P1,P6-Di(adenosine-5') hexaphosphate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.18 M Magnesium Cloride, 19%(v/v) PEG 400, 10%(v/v) Glycerol, 0.09 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.75	α = 90
b = 91.75	β = 90
c = 169.703	γ = 90

Symmetry
Space Group	I 4 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	CCD	ADSC QUANTUM 210r	MIRRORS	2009-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97918	APS	19-BM

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	1.75	50	100	0.064	0.064	40.75	13.6		36814		-3	23.9

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	1.75	1.78	100		0.807	0.807	2.5	12.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1KYH	1.75	50	36814	1840	99.95	0.155	0.154	0.175	RANDOM	28.438

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]
-0.65			-0.65		1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.765
r_dihedral_angle_4_deg	17.591
r_dihedral_angle_3_deg	12.259
r_dihedral_angle_1_deg	6.516
r_scangle_it	5.034
r_angle_other_deg	4.231
r_scbond_it	3.09
r_mcangle_it	1.903
r_angle_refined_deg	1.746
r_mcbond_it	1.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.765
r_dihedral_angle_4_deg	17.591
r_dihedral_angle_3_deg	12.259
r_dihedral_angle_1_deg	6.516
r_scangle_it	5.034
r_angle_other_deg	4.231
r_scbond_it	3.09
r_mcangle_it	1.903
r_angle_refined_deg	1.746
r_mcbond_it	1.067
r_chiral_restr	0.111
r_bond_refined_d	0.02
r_gen_planes_other	0.012
r_gen_planes_refined	0.01
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2107
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	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.