1NFB | pdb_00001nfb

Ternary complex of the human type II Inosine Monophosphate Dedhydrogenase with 6Cl-IMP and NAD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B3O	Chain A of PDB ENTRY 1B3O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	8% PEG 6000, 0.1M Tris-HCl, 24mM beta-mercaptoethanol, 1M LiCl, 20% Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
4.06	69.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.19	α = 90
b = 145.19	β = 90
c = 127.1	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	93	CCD	ADSC QUANTUM 4	mirrors	2002-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.93	CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.9	51.33	85.1	0.034	0.034	17.37	2.7	29280	24775			39.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.98	81		0.343	0.343	2.3	2.6	1757

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	Chain A of PDB ENTRY 1B3O	2.9	47.82	1.1	29280	19483	1964	66.5	0.291	0.229	0.229	0.245	0.274	0.2665	RANDOM	59.1

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]
-4.78			-4.78		9.57

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.2
c_scangle_it	12.7
c_mcangle_it	9.71
c_scbond_it	8.14
c_mcbond_it	5.62
c_angle_deg	1.6
c_improper_angle_d	0.95
c_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5666
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	132

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling
MOLREP	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.