4YP6 | pdb_00004yp6

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
4.08	69.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.467	α = 90
b = 124.467	β = 90
c = 112.383	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		2001-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	1.1000	NSLS	X8C

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	1.9	28.89	98.2	0.078	11.83	1.52		78167

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	1.9	1.99	97.8		0.471	3.68	1.48

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	1.9	20	74179	3928	98.22	0.176	0.1753	0.19	0.1883	0.2	RANDOM	27.323

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]
-0.12	-0.06		-0.12		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.514
r_dihedral_angle_4_deg	16.151
r_dihedral_angle_3_deg	12.472
r_dihedral_angle_1_deg	5.581
r_mcangle_it	2.541
r_mcbond_other	1.792
r_mcbond_it	1.791
r_angle_refined_deg	1.568
r_angle_other_deg	1.353
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.514
r_dihedral_angle_4_deg	16.151
r_dihedral_angle_3_deg	12.472
r_dihedral_angle_1_deg	5.581
r_mcangle_it	2.541
r_mcbond_other	1.792
r_mcbond_it	1.791
r_angle_refined_deg	1.568
r_angle_other_deg	1.353
r_chiral_restr	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4053
Nucleic Acid Atoms
Solvent Atoms	497
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.