4YP7

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

Crystal Properties
Matthews coefficient	Solvent content
4.06	69.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.448	α = 90
b = 124.448	β = 90
c = 111.943	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	2.3	14.99	93.1	0.06	18.8	1.56		41867

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	2.3	2.4	93.3		0.217	6.09	1.58

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	1EJ2	2.3	20	39652	2202	93.16	0.1909	0.19	0.2083	RANDOM	26.88

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]
-0.62	-0.31		-0.62		2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.93
r_dihedral_angle_4_deg	17.972
r_dihedral_angle_3_deg	14.175
r_dihedral_angle_1_deg	5.458
r_mcangle_it	2.415
r_mcbond_it	1.632
r_mcbond_other	1.632
r_angle_refined_deg	1.566
r_angle_other_deg	1.359
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.93
r_dihedral_angle_4_deg	17.972
r_dihedral_angle_3_deg	14.175
r_dihedral_angle_1_deg	5.458
r_mcangle_it	2.415
r_mcbond_it	1.632
r_mcbond_other	1.632
r_angle_refined_deg	1.566
r_angle_other_deg	1.359
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4000
Nucleic Acid Atoms
Solvent Atoms	155
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 R01GM133198.