3DAU | pdb_00003dau

Crystal structure of the ternary MTX NADPH complex of Escherichia coli dihydrofolate reductase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RH3	PDB entry 1RH3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.847	α = 90
b = 61.847	β = 90
c = 104.74	γ = 120

Symmetry
Space Group	P 32 2 1

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	Bent conical mirror	2005-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90000	APS	14-BM-C

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	1.35	20	98.6	0.059	16.7	5.5	55916	50833	1	1

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	1.35	1.4	98.4		0.921	1.24	2.9	5001

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 1RH3	1.5	18.88	1	1	37199	35313	1886	98.45	0.16	0.159	0.17	0.186	0.19	RANDOM	26.06

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]
0.1	0.05		0.1		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.601
r_dihedral_angle_4_deg	14.319
r_sphericity_free	13.658
r_dihedral_angle_3_deg	13.389
r_sphericity_bonded	9.78
r_dihedral_angle_1_deg	5.846
r_scangle_it	5.287
r_scbond_it	4.1
r_mcangle_it	2.992
r_rigid_bond_restr	2.513
r_angle_refined_deg	2.219
r_mcbond_it	2.212
r_symmetry_vdw_refined	0.388
r_nbtor_refined	0.31
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.174
r_chiral_restr	0.144
r_xyhbond_nbd_refined	0.112
r_bond_refined_d	0.022
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1246
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	81

Software

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