2W3V

MYCOBACTERIUM AVIUM DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RX1	PDB ENTRY 1RX1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	MAVDHFR (15 MG/ML) IN 20 MM HEPES (PH 7.0), 1 MM DTT, 0.1 MM EDTA, 1.5 MM NAN3 WAS MIXED WITH NADPH (3 MM, 15 MIN AT ROOM TEMPERATURE) AND THEN TRIMETHOPRIM (2 MM, 15 MIN ON ICE). CRYSTALLIZATION (HANGING DROP VAPOR PHASE EQUILIBRATION) WAS ACHIEVED BY MIXING WITH AN EQUAL VOLUME OF THE PROTEIN COMPLEX WITH A RESERVOIR SOLUTION CONSISTING OF 70% 2-METHYL-2, 4-PENTANEDIOL (MPD) AND 100 MM HEPES (PH 6.5), AND SUSPENDING THE MIXTURE OVER THE RESERVOIR AT 277 K. SMALL ROD-LIKE CRYSTALS (0.01 X 0.01 X 0.05 MM) GREW WITHIN 2 DAYS. CRYSTALS WERE FLASH-COOLED DIRECTLY FROM THE DROP IN LIQUID N2.

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.816	α = 90
b = 70.816	β = 90
c = 73.613	γ = 90

Symmetry
Space Group	P 41 21 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	IMAGE PLATE	MARRESEARCH	MIRRORS	2000-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.785	SSRL	BL9-1

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	1.89	15	98.2	0.07	11.2	4.6		15319		-10	24.8

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	1.89	1.95	90.5		0.54	2.7	4.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1RX1	1.89	14.83	14529	773	98.3	0.182	0.18	0.224	RANDOM	29.52

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]
1.17			1.17		-2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.172
r_dihedral_angle_4_deg	16.73
r_dihedral_angle_3_deg	12.153
r_dihedral_angle_1_deg	5.902
r_scangle_it	3.31
r_scbond_it	2.274
r_angle_refined_deg	1.553
r_mcangle_it	1.395
r_mcbond_it	0.904
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.2
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1276
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing