3RRB | pdb_00003rrb

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

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
2.62	53.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.102	α = 90
b = 122.102	β = 90
c = 155.614	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	MARMOSAIC 300 mm CCD	MIRRORS	2008-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12712	APS	21-ID-D

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	2.4	50	99.8	0.07	0.07	38.523	8.7	200896	200896		-3	58.9

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	2.4	2.44	98.9		0.938	0.938	1.814	5.7

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	2.4	50	23145	1193	99.49	0.17	0.167	0.17	0.216	0.22	RANDOM	58.275

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]
-0.83			-0.83		1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.863
r_dihedral_angle_4_deg	16.037
r_dihedral_angle_3_deg	15.562
r_dihedral_angle_1_deg	6.329
r_scangle_it	4.222
r_angle_other_deg	4.22
r_scbond_it	2.533
r_angle_refined_deg	1.706
r_mcangle_it	1.471
r_mcbond_it	0.752

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.863
r_dihedral_angle_4_deg	16.037
r_dihedral_angle_3_deg	15.562
r_dihedral_angle_1_deg	6.329
r_scangle_it	4.222
r_angle_other_deg	4.22
r_scbond_it	2.533
r_angle_refined_deg	1.706
r_mcangle_it	1.471
r_mcbond_it	0.752
r_chiral_restr	0.096
r_bond_refined_d	0.02
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3773
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	47

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.