3QLY | pdb_00003qly

Candida glabrata dihydrofolate reductase complexed with NADPH and 6-methyl-5-[3-methyl-3-(3,4,5-trimethoxyphenyl)but-1-yn-1-yl]pyrimidine-2,4-diamine (UCP115A)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CSE	PDB ENTRY 3CSE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	PEG 4000, MgCl2, Tris, pH 8.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.731	α = 90
b = 42.731	β = 90
c = 230.839	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	ADSC QUANTUM 315	mirrors	2010-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.100	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	2.519	50	99.9	0.108	9.2	5.3	13749	13749	3	3

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	2.519	2.65	100		0.413		5.1	1352

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-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 3CSE	2.519	30.22	13749	13749	690	99.13	0.2136	0.2136	0.2108	0.21	0.2674	0.26	RANDOM	30.9484

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		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.944
r_dihedral_angle_4_deg	16.999
r_dihedral_angle_3_deg	13.516
r_dihedral_angle_1_deg	5.171
r_scangle_it	2.122
r_scbond_it	1.322
r_mcangle_it	0.976
r_angle_refined_deg	0.697
r_mcbond_it	0.562
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.944
r_dihedral_angle_4_deg	16.999
r_dihedral_angle_3_deg	13.516
r_dihedral_angle_1_deg	5.171
r_scangle_it	2.122
r_scbond_it	1.322
r_mcangle_it	0.976
r_angle_refined_deg	0.697
r_mcbond_it	0.562
r_nbtor_refined	0.32
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.135
r_symmetry_hbond_refined	0.065
r_chiral_restr	0.058
r_gen_planes_refined	0.007
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3692
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	148

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction

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.