1VRD

Crystal structure of Inosine-5'-monophosphate dehydrogenase (TM1347) from THERMOTOGA MARITIMA at 2.18 A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	4	273	40% MPD, 0.1M citric acid pH 4.0, final pH 4, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.083	α = 90
b = 120.083	β = 90
c = 144.079	γ = 90

Symmetry
Space Group	I 4

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		2001-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3		ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.18	46.12	94.49	0.078	14.26	4.11		50043			44.79

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.2	75.52		0.574	1.51	3.26	1308

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	1zfj	2.18	46.12	47472	2553	94.22	0.21863	0.21653	0.25759	RANDOM	39.358

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]
-2.2			-2.2		4.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.071
r_dihedral_angle_4_deg	16.725
r_dihedral_angle_3_deg	15.276
r_scangle_it	8.37
r_scbond_it	6.057
r_dihedral_angle_1_deg	5.935
r_mcangle_it	3.083
r_mcbond_it	2.073
r_angle_refined_deg	1.523
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.071
r_dihedral_angle_4_deg	16.725
r_dihedral_angle_3_deg	15.276
r_scangle_it	8.37
r_scbond_it	6.057
r_dihedral_angle_1_deg	5.935
r_mcangle_it	3.083
r_mcbond_it	2.073
r_angle_refined_deg	1.523
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4670
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

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.