3RQ2 | pdb_00003rq2

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADH

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	0.005 M ATP, 0.18 M Magnesium Cloride, 13.5%(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
2.97	58.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.93	α = 90
b = 91.93	β = 90
c = 169.626	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	1.8	50	100	0.083	0.083	45.786	13.4		33796		-3	31.5

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	1.8	1.83	99.9		0.896	0.896	1.895	11.8

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 1KYH	1.8	50	33796	1716	99.91	0.154	0.153	0.16	0.178	0.19	RANDOM	36.61

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]
-1.49			-1.49		2.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.831
r_dihedral_angle_4_deg	16.214
r_dihedral_angle_3_deg	12.283
r_dihedral_angle_1_deg	6.57
r_angle_other_deg	4.221
r_scangle_it	4.175
r_scbond_it	2.645
r_angle_refined_deg	1.757
r_mcangle_it	1.653
r_mcbond_it	0.976

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.831
r_dihedral_angle_4_deg	16.214
r_dihedral_angle_3_deg	12.283
r_dihedral_angle_1_deg	6.57
r_angle_other_deg	4.221
r_scangle_it	4.175
r_scbond_it	2.645
r_angle_refined_deg	1.757
r_mcangle_it	1.653
r_mcbond_it	0.976
r_chiral_restr	0.102
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_gen_planes_other	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	184
Heterogen Atoms	69

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.