3JTW | pdb_00003jtw

Crystal structure of Putative dihydrofolate reductase (YP_805003.1) from PEDIOCOCCUS PENTOSACEUS ATCC 25745 at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.9	277	2.0000M (NH4)2SO4, 5.0000% iso-Propanol, 0.1M Citrate pH 4.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.759	α = 90
b = 83.314	β = 90
c = 65.059	γ = 90

Symmetry
Space Group	P 21 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	CCD	MARMOSAIC 325 mm CCD	Flat mirror, vertical and horizontal focussing mirrors	2009-05-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.91162,0.97943,0.97959	SSRL	BL12-2

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	1.9	29.476	99.8	0.107	0.107	8.5	4		30501			20.63

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	1.9	1.95	100		0.598	0.598	1.2	4	2227

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.9	29.476	30477	1539	99.69	0.184	0.182	0.1859	0.225	0.2283	RANDOM	26.844

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]
-0.11			1.59		-1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.681
r_dihedral_angle_4_deg	18.018
r_dihedral_angle_3_deg	15.287
r_dihedral_angle_1_deg	6.402
r_scangle_it	4.445
r_scbond_it	3.402
r_mcangle_it	2.643
r_mcbond_it	2.032
r_angle_refined_deg	1.569
r_angle_other_deg	0.966
r_mcbond_other	0.68
r_symmetry_vdw_other	0.261
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.197
r_nbd_other	0.191
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.119
r_chiral_restr	0.098
r_nbtor_other	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2814
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction