3EEK | pdb_00003eek

Candida glabrata Dihydrofolate Reductase complexed with 2,4-diamino-5-[3-methyl-3-(3-methoxy-5-(4-methylphenyl)phenyl)prop-1-ynyl]-6-methylpyrimidine(UCP111D4M) and NADPH

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	PEG4000, MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.753	α = 90
b = 42.753	β = 90
c = 230.448	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD			2008-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.04	50	90.7	0.067	16.556	3.1		23938

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.04	2.11	58.7		0.291		1.6	1508

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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		THROUGHOUT	2.03	42.76	23937	1223	90.89	0.178	0.175	0.18	0.243	0.24	RANDOM	21.952

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			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.124
r_dihedral_angle_1_deg	31.021
r_dihedral_angle_4_deg	18.933
r_dihedral_angle_3_deg	17.299
r_scangle_it	4.499
r_scbond_it	3.23
r_angle_refined_deg	2.329
r_mcangle_it	1.828
r_mcbond_it	1.652
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.124
r_dihedral_angle_1_deg	31.021
r_dihedral_angle_4_deg	18.933
r_dihedral_angle_3_deg	17.299
r_scangle_it	4.499
r_scbond_it	3.23
r_angle_refined_deg	2.329
r_mcangle_it	1.828
r_mcbond_it	1.652
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.271
r_symmetry_hbond_refined	0.271
r_nbd_refined	0.221
r_chiral_restr	0.191
r_xyhbond_nbd_refined	0.144
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3692
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	152

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.