2B1I

crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G8M	PDB entry 1G8M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	295	PEG 8000, imidazole, DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56	α = 90
b = 106.5	β = 91.5
c = 101	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 4		2004-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.99997	ALS	8.2.1

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	2.02	50	97.1	0.065	24.8	2.5		75375			31.2

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	2.02	2.09	91.5	91.5	0.275	2.8	2	7071

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1G8M	2.02	38.07	75375	69574	1744	92.33	0.251	0.199	0.198	0.249	RANDOM	41.161

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]
2.98		-0.13	1.91		-4.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.433
r_dihedral_angle_4_deg	19.813
r_dihedral_angle_3_deg	16.187
r_dihedral_angle_1_deg	5.888
r_scangle_it	2.855
r_scbond_it	1.828
r_angle_refined_deg	1.471
r_mcangle_it	0.999
r_mcbond_it	0.546
r_symmetry_hbond_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.433
r_dihedral_angle_4_deg	19.813
r_dihedral_angle_3_deg	16.187
r_dihedral_angle_1_deg	5.888
r_scangle_it	2.855
r_scbond_it	1.828
r_angle_refined_deg	1.471
r_mcangle_it	0.999
r_mcbond_it	0.546
r_symmetry_hbond_refined	0.315
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.224
r_metal_ion_refined	0.178
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9022
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	102

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.