4YP5 | pdb_00004yp5

Crystal structure of Methanobacterium thermoautotrophicum NMNAT in complex with NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EJ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	ammonium sulfate, glycerol, TRIS, NADP

Crystal Properties
Matthews coefficient	Solvent content
4.07	69.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.586	α = 90
b = 124.586	β = 90
c = 111.959	γ = 120

Symmetry
Space Group	P 31 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	ADSC QUANTUM 4		2000-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	1.0000	APS	14-BM-C

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	2.21	20	89.3	0.052	15.68	1.27		45535

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	2.21	2.31	87		0.255	4.84	1.15

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	1EJ2	2.21	20	43177	2356	89.37	0.1814	0.1806	0.19	0.1955	0.2	RANDOM	37.612

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]
-0.45	-0.23		-0.45		1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.583
r_dihedral_angle_4_deg	16.372
r_dihedral_angle_3_deg	13.913
r_dihedral_angle_1_deg	5.533
r_mcangle_it	3.378
r_mcbond_it	2.409
r_mcbond_other	2.409
r_angle_refined_deg	1.586
r_angle_other_deg	1.341
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.583
r_dihedral_angle_4_deg	16.372
r_dihedral_angle_3_deg	13.913
r_dihedral_angle_1_deg	5.533
r_mcangle_it	3.378
r_mcbond_it	2.409
r_mcbond_other	2.409
r_angle_refined_deg	1.586
r_angle_other_deg	1.341
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4033
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.