3EIG | pdb_00003eig

Crystal structure of a methotrexate-resistant mutant of human dihydrofolate reductase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U72	PDB ENTRY 1U72

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	0.2 M sodium dihydrogen phosphate, 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.348	α = 90
b = 47.868	β = 90
c = 90.715	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	93	IMAGE PLATE	RIGAKU RAXIS IV++	Osmic Confocal Blue	2008-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	1.7	50	97.2	0.064	0.064	14.6	11.7	20461	20461			21.584801

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	1.7	1.76	93.9		0.473	0.473		9.5	1941

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 1U72	1.7	10.52	20304	20304	2066	97.26	0.17929	0.17929	0.17442	0.172	0.22297	0.2193	RANDOM	16.372

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]
-0.13			-0.07		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.599
r_dihedral_angle_4_deg	20.37
r_dihedral_angle_3_deg	11.879
r_dihedral_angle_1_deg	6.074
r_scangle_it	2.591
r_scbond_it	1.73
r_angle_refined_deg	1.417
r_mcangle_it	1.081
r_mcbond_it	0.736
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1464
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	74

Software

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