3TYD | pdb_00003tyd

Dihydropteroate Synthase in complex with PPi and DHP+

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	291	LITHIUM SULFATE, Bis-Tris propane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.44	α = 90
b = 99.44	β = 90
c = 262.13	γ = 120

Symmetry
Space Group	P 62 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 300 mm CCD		2011-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	50	92.4	0.085	23.6	7.3		25528		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	70.1		0.214	2	5.8	1858

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	PDB ENTRY 1TWS	2.5	49.72	25433	1283	92.57	0.2268	0.2243	0.2209	0.2777	0.2716	RANDOM	81.9003

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]
4.78	2.39		4.78		-7.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.241
r_dihedral_angle_4_deg	20.511
r_dihedral_angle_3_deg	19.333
r_dihedral_angle_1_deg	5.792
r_scangle_it	3.08
r_scbond_it	1.889
r_angle_refined_deg	1.462
r_mcangle_it	1.153
r_mcbond_it	0.575
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4135
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling