3NXY | pdb_00003nxy

Preferential Selection of Isomer Binding from Chiral Mixtures: Alernate Binding Modes Observed fro 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

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U72	PDB entry 1u72

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	287	100 mM K2PO4, 60 % saturated ammonium sulfate, 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.424	α = 90
b = 84.424	β = 90
c = 77.348	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	1.9	53.3	100	0.278	0.307	5.3	5.6	19048	15398	2	2	32

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)
	1.9		100		0.033	0.037	0.6	5.6	2789

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB entry 1u72	1.9	53.15	2	2	19048	15398	796	99.99	0.21718	0.21441	0.2138	0.27033	0.2677	RANDOM	24.572

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.41
r_dihedral_angle_3_deg	18.89
r_dihedral_angle_4_deg	15.184
r_dihedral_angle_1_deg	7.183
r_scangle_it	4.422
r_scbond_it	3.055
r_angle_refined_deg	2.097
r_mcangle_it	1.918
r_mcbond_it	1.12
r_chiral_restr	0.136
r_bond_refined_d	0.022
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1502
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	83

Software

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