3NXO | pdb_00003nxo

Perferential Selection of Isomer Binding from Chiral Mixtures: Alternate Binding Modes Observed for the E- and Z-isomers of a Series of 5-Substituted 2,4-Diaminofuro[2,3-d]pyrimidines as Ternary Complexes with NADPH and Human Dihydrofolate Reductase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U70	PDB entry 1u70.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	298	K2PO4 with 30% saturated ammonium sulfate with 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.15	α = 90
b = 84.15	β = 90
c = 77.968	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	MARMOSAIC 325 mm CCD	mirrors	2008-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.975	SSRL	BL9-2

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	1.35	26.6	99.9	0.068	0.025	18.9	8.7	45729	45197	2	2	20.1

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	1.35	1.42	99.9		0.5	0.17	4.4	8.2	6605

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	PDB entry 1u70.pdb	1.35	26.62	2	45197	42917	2276	99.94	0.1967	0.19223	0.19132	0.1927	0.20892	0.2058	RANDOM	16.678

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.888
r_dihedral_angle_4_deg	18.495
r_dihedral_angle_3_deg	14.454
r_dihedral_angle_1_deg	7.071
r_scangle_it	5.297
r_scbond_it	3.618
r_angle_refined_deg	2.788
r_mcangle_it	2.491
r_mcbond_it	1.492
r_chiral_restr	0.176

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.888
r_dihedral_angle_4_deg	18.495
r_dihedral_angle_3_deg	14.454
r_dihedral_angle_1_deg	7.071
r_scangle_it	5.297
r_scbond_it	3.618
r_angle_refined_deg	2.788
r_mcangle_it	2.491
r_mcbond_it	1.492
r_chiral_restr	0.176
r_bond_refined_d	0.034
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1504
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	97

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.