7MQP | pdb_00007mqp

E. coli dihydrofolate reductase complexed with 4'-chloro-3'-(4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl)-[1,1'-biphenyl]-4-carboxamide (UCP1228)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277.15	0.3-0.35 M lithium sulfate, 15-19% PEG 6,000

Crystal Properties
Matthews coefficient	Solvent content
3.76	67.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.681	α = 90
b = 66.681	β = 90
c = 213.752	γ = 120

Symmetry
Space Group	P 61 2 2

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	MARMOSAIC 325 mm CCD		2017-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.1	57.81	99.72	1	21.82	1.2		17232

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.102	2.177	100		1	3.73	1.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1RF7	2.1	57.81	16430	803	99.72	0.1923	0.1903	0.2	0.2327	0.25	RANDOM	65.274

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]
1.33	0.66		1.33		-4.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.18
r_dihedral_angle_4_deg	20.181
r_dihedral_angle_3_deg	16.994
r_dihedral_angle_1_deg	6.689
r_angle_refined_deg	2.017
r_angle_other_deg	1.088
r_chiral_restr	0.108
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.18
r_dihedral_angle_4_deg	20.181
r_dihedral_angle_3_deg	16.994
r_dihedral_angle_1_deg	6.689
r_angle_refined_deg	2.017
r_angle_other_deg	1.088
r_chiral_restr	0.108
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1284
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	65

Software

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

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.