3RSS | pdb_00003rss

Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AX3	PDB ENTRY 2AX3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M Na Cacodylate, 1.6 M Na Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.271	α = 90
b = 122.271	β = 90
c = 154.879	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 315	MIRRORS	2009-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97857	APS	19-ID

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	1.95	50	99.7	0.059	0.059	39.959	9.5	42771	42559		-3	31.1

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	1.95	1.98	100		0.717	0.717	2.62	9.2

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 2AX3	1.953	50	42559	2145	99.52	0.16	0.159	0.17	0.197	0.2	RANDOM	37.94

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]
-0.59			-0.59		1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.545
r_dihedral_angle_4_deg	13.816
r_dihedral_angle_3_deg	13.734
r_dihedral_angle_1_deg	6.067
r_scangle_it	5.26
r_angle_other_deg	4.191
r_scbond_it	3.153
r_mcangle_it	1.919
r_angle_refined_deg	1.69
r_mcbond_it	1.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.545
r_dihedral_angle_4_deg	13.816
r_dihedral_angle_3_deg	13.734
r_dihedral_angle_1_deg	6.067
r_scangle_it	5.26
r_angle_other_deg	4.191
r_scbond_it	3.153
r_mcangle_it	1.919
r_angle_refined_deg	1.69
r_mcbond_it	1.059
r_chiral_restr	0.11
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_gen_planes_other	0.008
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3829
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	41

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.