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HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 6-([5-QUINOLYLAMINO]METHYL)-2,4-DIAMINO-5-METHYLPYRIDO[2,3-D]PYRIMIDINE (SRI-9439), A LIPOPHILIC ANTIFOLATE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
other
UNPUBLISHED HUMAN DHFR STRUCTURE.
Crystallization
Crystalization Experiments
ID
Method
pH
Temperature
Details
1
VAPOR DIFFUSION, HANGING DROP
8
277
THE TERNARY COMPLEX OF DHFR
WITH NADPH AND SRI-9439 WAS FORMED BY MIXING HUMAN DHFR
(20 MG/ML IN 25 MM KPO4 (PH 7.0), 0.1 MM EDTA, AND 3 MM
NAN3) WITH 60 MM NADPH, FOLLOWED 15 MINUTES LATER BY 60 MM
OF INHIBITOR IN DMSO (FINAL CONCENTRATIONS OF 2 MM NADPH
AND 2 MM INHIBITOR). THIS COMPLEX SOLUTION WAS MIXED WITH
AN EQUAL VOLUME OF PRECIPITANT CONTAINING 24-33% PEG 4000,
0.2 M LI2SO4, 0.1 M TRIS CL (PH 7.9-8.4), AND EQUILIBRATED
WITH THE PRECIPITANT BY HANGING DROP VAPOR DIFFUSION AT
277 K. THE CRYSTAL GREW IN ABOUT 3 WEEKS. THE CRYSTAL WAS
FLASH-COOLED DIRECTLY IN LIQUID NITROGEN AFTER HARVESTING
INTO MOTHER LIQUOR CONTAINING 10% GLYCEROL., pH 8.00, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficient
Solvent content
2.23
46
Crystal Data
Unit Cell
Length ( Å )
Angle ( ˚ )
a = 41.467
α = 90
b = 55.275
β = 90
c = 82.799
γ = 90
Symmetry
Space Group
P 21 21 21
Diffraction
Diffraction Experiment
ID #
Crystal ID
Scattering Type
Data Collection Temperature
Detector
Detector Type
Details
Collection Date
Monochromator
Protocol
1
1
x-ray
100
IMAGE PLATE
MARRESEARCH
PT-COATED MIRROR
1997-06-25
M
SINGLE WAVELENGTH
Radiation Source
ID #
Source
Type
Wavelength List
Synchrotron Site
Beamline
1
SYNCHROTRON
SSRL BEAMLINE BL7-1
SSRL
BL7-1
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
1.09
20
99.6
0.047
0.047
9.4
3.6
79611
79611
10.8
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)
1.09
1.15
99.1
0.422
0.422
2.3
3.3
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-Work (Depositor)
R-Work (DCC)
R-Free (Depositor)
R-Free (DCC)
R-Free Selection Details
Mean Isotropic B
X-RAY DIFFRACTION
MOLECULAR REPLACEMENT
THROUGHOUT
UNPUBLISHED HUMAN DHFR STRUCTURE.
1.09
20
79411
79411
3988
99.6
0.1306
0.1409
0.1726
0.1703
5% OF THE REFLECTIONS WERE RANDOMLY SELECTED FOR THE TEST SET.